Chemical and molecular characterization of Phomopsis and Cytospora-like endophytes from different host plants in Brazil

Untargeted metabolomic analyses support the main phylogenetic groups of the common plant-associated Alternaria fungi isolated from grapevine (Vitis vinifera)

Alternaria, a cosmopolitan fungal genus is a dominant member of the grapevine (Vitis vinifera) microbiome. Several Alternaria species are known to produce a variety of secondary metabolites, which are particularly relevant to plant protection and food safety in field crops. According to previous findings, the majority of Alternaria species inhabiting grapevine belong to Alternaria sect. Alternaria. However, the phylogenetic diversity and secondary metabolite production of the distinct Alternaria species has remained unclear. In this study, our aim was to examine the genetic and metabolic diversity of endophytic Alternaria isolates associated with the above-ground tissues of the grapevine. Altogether, 270 Alternaria isolates were collected from asymptomatic leaves and grape clusters of different grapevine varieties in the Eger wine region of Hungary. After analyses of the nuclear ribosomal DNA internal transcribed spacer (ITS) and RNA polymerase second largest subunit (rpb2) sequences, 170 isolates were chosen for further analyses. Sequences of the Alternaria major allergen gene (Alt a 1), endopolygalacturonase (endoPG), OPA10-2, and KOG1058 were also included in the phylogenetic analyses. Identification of secondary metabolites and metabolite profiling of the isolates were performed using high-performance liquid chromatography (HPLC)-high-resolution tandem mass spectrometry (HR-MS/MS). The multilocus phylogeny results revealed two distinct groups in grapevine, namely A. alternata and the A. arborescens species complex (AASC). Eight main metabolites were identified in all collected Alternaria isolates, regardless of their affiliation to the species and lineages. Multivariate analyses of untargeted metabolites found no clear separations; however, a partial least squares-discriminant analysis model was able to successfully discriminate between the metabolic datasets from isolates belonging to the AASC and A. alternata. By conducting univariate analysis based on the discriminant ability of the metabolites, we also identified several features exhibiting large and significant variation between A. alternata and the AASC. The separation of these groups may suggest functional differences, which may also play a role in the functioning of the plant microbiome.

Antimicrobial properties and biotransforming ability of fungal endophytes from Ficus carica L. (Moraceae)

The endophytic fungal community associated with leaves of Ficus carica L. (Moraceae) from Argentina was investigated. Fifteen fungal isolates were isolated and identified by molecular methods into the genera Alternaria, Cladosporium, Curvularia, Diaporthe, Epicoccum, Myrothecium, Neofusicoccum, Nigrospora, Preussia and Ustilago. Cladosporium cladosporioides and Curvularia lunata were the most frequently isolated species. The fungal metabolic profiles were obtained by automated TLC and NMR and analysed by PC Analysis. Antifungal and antibacterial activity was assessed by bioautographic assays. In addition, the biotransforming ability of the fungal isolates was tested on F. carica extracts. Five isolates (33.3%) exhibited inhibitory activity against at least one of the microorganisms tested. Most of the fungal endophytes were able to metabolise the flavonoid rutin 1, and the coumarin psoralen 3 present in F. carica extracts. Further investigations of the psoralen biotransforming ability performed by the selected endophyte Alternaria alternata F8 showed the accumulation of the 6,7-furan-hydrocoumaric acid derivative 4 as the main biotransformation product. Our results corroborate that F. carica can live symbiotically with rich and diverse endophytic communities adding insights about their ecological interactions.

Pioneering Metabolomic Studies on Diaporthe eres Species Complex from Fruit Trees in the South-Eastern Poland

Fungi from the genus Diaporthe have been reported as plant pathogens, endophytes, and saprophytes on a wide range of host plants worldwide. Their precise identification is problematic since many Diaporthe species can colonize a single host plant, whereas the same Diaporthe species can inhabit many hosts. Recently, Diaporthe has been proven to be a rich source of bioactive secondary metabolites. In our initial study, 40 Diaporthe isolates were analyzed for their metabolite production. A total of 153 compounds were identified based on their spectroscopic properties-Ultraviolet-visible and mass spectrometry. From these, 43 fungal metabolites were recognized as potential chemotaxonomic markers, mostly belonging to the drimane sesquiterpenoid-phthalide hybrid class. This group included mainly phytotoxic compounds such as cyclopaldic acid, altiloxin A, B, and their derivatives. To the best of our knowledge, this is the first report on the metabolomic studies on Diaporthe eres species complex from fruit trees in the South-Eastern Poland. The results from our study may provide the basis for the future research on the isolation of identified metabolites and on their bioactive potential for agricultural applications as biopesticides or biofertilizers.

Fungal endophytes in Peperomia obtusifolia and their potential as inhibitors of chickpea fungal pathogens

Chickpea (Cicer arietinum L., Fabaceae) is the second most important legume after common bean (Phaseolus vulgaris L., Fabaceae) and third in production among the legumes grains worldwide. Ascochyta blight and Fusarium wilt are among the main fungal infections which cause the major losses of chickpea crop. In this work we report the phyto-pathogen controlling properties of 24 endophyte Phomopsis/Diaporthe isolates on the chickpea fungal pathogens Ascochyta rabiei, Fusarium oxysporum and Fusarium solani. The Phomopsis/Diaporthe strains were isolated amongst a total of 62 endophytic fungi from the aerial parts of the herbaceous perennial American plant Peperomia obtusifolia (Piperaceae) along with Fusarium, Septoria, Colletotrichum, Alternaria and Roussoella genera among others. Phomopsis/Diaporthe isolates were identified as Diaporthe infecunda (12 isolates), Diaporthe sackstoni (1 isolate), Diaporthe cf. brasiliensis (4 isolates) and Phomopsis cf. tuberivora (7 isolates). All the Phomopsis/Diaporthe strains antagonized A. rabiei strain AR2 with a mean of inhibition (% I) of 86.59 ± 1.49% in dual cultures. The metabolic characterization of the Phomopsis/Diaporthe strains showed groups in three clusters which were in agreement with the taxonomic identification. Bioautographic evaluation of organic extracts showed that those of D. cf. brasiliensis and D. infecunda were better as inhibitors. Strain Po 45 was one of the most active (cluster 1, 96.87% I), and its ethyl acetate extract inhibited A. rabiei growth in a bioautographic assay until at least 10 μg/mm applied showing a specific chromatographic band as the responsible of the A. rabiei inhibition.

Natural Products from Endophytic Fungi Associated with Rubiaceae Species

This review presents the chemical diversity and pharmacological properties of secondary metabolites produced by endophytic fungi associated with various genera of Rubiaceae. Several classes of natural products are described for these endophytes, although, this study highlights the importance of some metabolites, which are involved in antifungal, antibacterial, anti-protozoal activities; neurodegenerative diseases; cytotoxic activity; anti-inflammatory and antioxidant activity; and hyperglycemic control.

Diversity and bioactivities of fungal endophytes from Distylium chinense, a rare waterlogging tolerant plant endemic to the Three Gorges Reservoir

BACKGROUND

The present study involves diversity and biological activities of the endophytic fungal community from Distylium chinense, a rare waterlogging tolerant plant endemic to the Three Gorges Reservoir. This study has been conducted hypothesizing that the microbial communities in the TGR area would contribute to the host plant tolerating a range of abiotic stress such as summer flooding, infertility, drought, salinity and soil erosion etc., and they may produce new metabolites, which may possess plentiful bioactive property, especially antioxidant activity. Therefore in the current study, the antioxidant, antimicrobial and anticancer activities of 154 endophytes recovered from D. chinense have been investigated. Furthermore, the active metabolites of the most broad-spectrum bioactive strain have also been studied.

RESULTS

A total of 154 fungal endophytes were isolated from roots and stems. They were categorized into 30 morphotypes based on cultural characteristics and were affiliated with 27 different taxa. Among these, the most abundant fungal orders included Diaporthales (34.4%) and Botryosphaeriales (30.5%), which were predominantly represented by the species Phomopsis sp. (24.7%) and Neofusicoccum parvum (23.4%). Fermentation extracts were evaluated, screening for antioxidant, antimicrobial and anticancer activities. Among the 154 isolates tested, 99 (64.3%) displayed significant antioxidant activity, 153 (99.4%) exhibited inclusive antimicrobial activity against at least one tested microorganism and 27 (17.5%) showed exclusive anticancer activity against one or more cancer cell lines. Specifically, the crude extract of Irpex lacteus DR10-1 exhibited note-worthy bioactivities. Further chemical investigation on DR10-1 strain resulted in the isolation and identification of two known bioactive metabolites, indole-3-carboxylic acid (1) and indole-3-carboxaldehyde (2), indicating their potential roles in plant growth promotion and human medicinal value.

CONCLUSION

These results indicated that diverse endophytic fungal population inhabits D. chinense. One of the fungal isolate DR10-1 (Irpex lacteus) exhibited significant antioxidant, antimicrobial and anticancer potential. Further, its active secondary metabolites 1 and 2 also showed antioxidant, antimicrobial and anticancer potential.

Multiloci identification of Diaporthe fungi isolated from the medicinal plant Costus spiralis (Jacq.) Roscoe (Costaceae)

AIMS

The purpose of this study is to identify species from genus Diaporthe associated with a medicinal plant Costus spiralis by ITS, EF 1-α, TUB and CAL gens.

METHODS AND RESULTS

The 30 isolates from the genus Diaporthe associated with the medicinal plant Costus spiralis were characterized based on morphological characters and the microculture technique and grouped by DNA fingerprinting with the ISSP gene. Afterwards, a total of 12 isolates were selected for the identification of the species based on the comparative research on the blast through the sequences of the ITS gene. Phylogenetic Tree of Maximum Likelihood were generated with the ITS gene individually and with the genes ITS, TUB, CAL and EF1-α combined with the Diaporthe species recognized and with the additional sequences obtained from GenBank for these species.

CONCLUSIONS

It was not possible to characterize the 30 isolates microscopically and macromorphologically through the microculture technique and the macromorphological characteristics. The 12 isolates selected based on the DNA fingerprinting profile identified phylogenetically, revealed five distinct species of Diaporthe which are present in C. spiralis.

SIGNIFICANCE AND IMPACT OF THE STUDY

The molecular analyses used in this study are excellent alternatives for species-level identification of Diaporthe associated with medicinal plants.

Metabolites Produced by an Endophytic Phomopsis sp. and Their Anti-TMV Activity

The fermentation and isolation of metabolites produced by an endophytic fungus, which was identified as Phomopsis sp. FJBR-11, based on phylogenetic analysis, led to the identification of six compounds, including dothiorelones A-C, and H, and cytosporones C and U. Among these compounds, cytosporone U exhibited potent inhibitory activity against Tobacco mosaic virus (TMV). Moreover, the crude and a purified exopolysaccharide were proved to possess strong inhibitory effects against the virus infection.

Biological activity of Diaporthe terebinthifolii extracts against Phyllosticta citricarpa

Citrus black spot disease, caused by the phytopathogen Phyllosticta citricarpa, depreciates the market value of citrus fruits and prevents their exportation to disease-free regions. It may also reduce the productivity of citrus fruit orchards. To identify an alternative to conventional disease control measures, isolates of Diaporthe terebinthifolii, active against P. citricarpa, were selected from an endophytic fungal population of Schinus terebinthifolia leaves. Different culture media were screened to identify the culture medium that afforded the most efficient production of biologically active extracts. A particular fraction (fraction VI) of the extract completely protected orange leaves by inhibiting the germination of P. citricarpa conidia with a minimum inhibitory concentration of 0.003 μg.mL-1. The active constituents in D. terebinthifolii extract fractions were identified by gas chromatography coupled to mass spectrometry as verbanol, phenylethyl alcohol, verbenyl acetate and methyl hexadecanoate. The results obtained strongly suggest the existence of a synergistic effect among the metabolites produced. Thus, these fungal metabolites could be used to control the CBS disease. As the asexual spores of P. citricarpa play an important role in fruit lesion development and disease dispersion, fungal extracts that inhibit the spore germination can be used as an effective alternative for directional disease control.

Isolation, characterization and toxicological potential of Alternaria-mycotoxins (TeA, AOH and AME) in different Alternaria species from various regions of India

Alternaria species produce various sorts of toxic metabolites during their active growth and causes severe diseases in many plants by limiting their productivity. These toxic metabolites incorporate various mycotoxins comprising of dibenzo-α-pyrone and some tetramic acid derivatives. In this study, we have screened out total 48 isolates of Alternaria from different plants belonging to different locations in India, on the basis of their pathogenic nature. Pathogenicity testing of these 48 strains on susceptible tomato variety (CO-3) showed 27.08% of the strains were highly pathogenic, 35.41% moderately pathogenic and 37.5% were less pathogenic. Phylogenetic analysis showed the presence of at least eight evolutionary cluster of the pathogen. Toxins (TeA, AOH and AME) were isolated, purified on the basis of column chromatography and TLC, and further confirmed by the HPLC-UV chromatograms using standards. The final detection of toxins was done by the LC-MS/MS analysis by their mass/charge ratio. The present study develops an approach to classify the toxicogenic effect of each of the individual mycotoxins on tomato plant and focuses their differential susceptibility to develop disease symptoms. This study represents the report of the natural occurrence and distribution of Alternaria toxins in various plants from India.

Genome-Guided Discovery of Natural Products and Biosynthetic Pathways from Australia’s Untapped Microbial Megadiversity

Historically microbial natural product biosynthesis pathways were elucidated mainly by isotope labelled precursor directed feeding studies. Now the genetics underpinning the assembly of microbial natural products biosynthesis is so well understood that some pathways and their products can be predicted from DNA sequences alone. The association between microbial natural products and their biosynthesis gene clusters is now driving the field of ‘genetics guided natural product discovery’. This account overviews our research into cyanotoxin biosynthesis before the genome sequencing era through to some recent discoveries resulting from the mining of Australian biota for natural product biosynthesis pathways.

Differential production of phytotoxins from Phomopsis sp. from grapevine plants showing esca symptoms

Nine strains of the fungus Phomopsis spp. were isolated from a vineyard showing decline from the disease esca. Strains were screened for their ability to produce secondary metabolites showing chemical diversity. The culture extracts of each strain were analyzed by liquid chromatography-ultraviolet-diode array detection-mass spectrometry. Three strains were selected for the isolation and characterization of eight of the major metabolites. Structures were elucidated by spectroscopic analyses including two-dimensional NMR and mass spectrometry and by comparison to literature data. Among the isolated metabolites were the known phomopsolide B (1), sydowinin A (6), sydowinol (7), cytosporone B (8), and four new furanones named phomopsolidones A-D (2-5). The fungal strains were identified as Phomopsis sp., Phomopsis viticola Sacc and, Phomopsis viticola complex. Biological assays on Vitis vinifera leaves and callus tissue, antibacterial, and insecticidal activities were evaluated. The results revealed variability regarding secondary metabolites with species of Phomopsis sp. associated with grapevine, raising the question of cultivar-driven strain selection and phytotoxins biosynthesis in grapevine plants.

Modulation of antimicrobial metabolites production by the fungus Aspergillus parasiticus

Biosynthesis of active secondary metabolites by fungi occurs as a specific response to the different growing environments. Changes in this environment alter the chemical and biological profiles leading to metabolites diversification and consequently to novel pharmacological applications. In this work, it was studied the influence of three parameters (fermentation length, medium composition and aeration) in the biosyntheses of antimicrobial metabolites by the fungus Aspergillus parasiticus in 10 distinct fermentation periods. Metabolism modulation in two culturing media, CYA and YES was evaluated by a 2(2) full factorial planning (ANOVA) and on a 2(3) factorial planning, role of aeration, medium composition and carbohydrate concentration were also evaluated. In overall, 120 different extracts were prepared, their HPLC profiles were obtained and the antimicrobial activity against A. flavus, C. albicans, E. coli and S. aureus of all extracts was evaluated by microdilution bioassay. Yield of kojic acid, a fine chemical produced by the fungus A. parasiticus was determined in all extracts. Statistical analyses pointed thirteen conditions able to modulate the production of bioactive metabolites by A. parasiticus. Effect of carbon source in metabolites diversification was significant as shown by the changes in the HPLC profiles of the extracts. Most of the extracts presented inhibition rates higher than that of kojic acid as for the extract obtained after 6 days of fermentation in YES medium under stirring. Kojic acid was not the only metabolite responsible for the activity since some highly active extracts showed to possess low amounts of this compound, as determined by HPLC.

Specificity of lipoxygenase pathways supports species delineation in the marine diatom genus Pseudo-nitzschia

Oxylipins are low-molecular weight secondary metabolites derived from the incorporation of oxygen into the carbon chains of polyunsaturated fatty acids (PUFAs). Oxylipins are produced in many prokaryotic and eukaryotic lineages where they are involved in a broad spectrum of actions spanning from stress and defense responses, regulation of growth and development, signaling, and innate immunity. We explored the diversity in oxylipin patterns in the marine planktonic diatom Pseudo-nitzschia. This genus includes several species only distinguishable with the aid of molecular markers. Oxylipin profiles of cultured strains were obtained by reverse phase column on a liquid chromatograph equipped with UV photodiode detector and q-ToF mass spectrometer. Lipoxygenase compounds were mapped on phylogenies of the genus Pseudo-nitzschia inferred from the nuclear encoded hyper-variable region of the LSU rDNA and the plastid encoded rbcL. Results showed that the genus Pseudo-nitzschia exhibits a rich and varied lipoxygenase metabolism of eicosapentaenoic acid (EPA), with a high level of specificity for oxylipin markers that generally corroborated the genotypic delineation, even among genetically closely related cryptic species. These results suggest that oxylipin profiles constitute additional identification tools for Pseudo-nitzschia species providing a functional support to species delineation obtained with molecular markers and morphological traits. The exploration of the diversity, patterns and plasticity of oxylipin production across diatom species and genera will also provide insights on the ecological functions of these secondary metabolites and on the selective pressures driving their diversification.

In silico analysis of diverse endophytic fungi by using ITS1-5,8S-ITS2 sequences with isolates from various plant families in Brazil

Brazil has a great diversity of plants, and considering that all plant species studied to date have endophytic microorganisms (bacteria or fungi), the country is a resource in the search for bioactive compounds. Endophytes live within plants without causing damage and may be in dynamic equilibrium with the health of the plant. Endophytic fungi can be identified by sequencing the region corresponding to internal transcribed spacer 1-5,8S-internal transcribed spacer 2 ribosomal DNA, and carrying out phylogenetic analyses of these sequences helps to identify species. The objective of this research was to perform in silico phylogenetic analysis of fungi isolated from various plant families in Brazil. For this study, we chose 12 articles published between 2005 and 2012 that examined endophytes isolated in Brazil. We analyzed sequences deposited in the National Center for Biotechnology Information GenBank database and carried out alignment to determine the genetic distance of strains using the Molecular Evolutionary Genetics Analysis version 5 program. The articles yielded 73 plant species belonging to 13 families found in the Brazilian States of Amazonas, Bahia, Minas Gerais, Paraná, and São Paulo. The use of GenBank and the Molecular Evolutionary Genetics Analysis program for phylogenetic observation revealed that several endophytes had been incorrectly identified because inconsistencies were apparent in their location in the phylogenetic tree. However, approximately 98% of the sequences deposited in GenBank were consistent with the identification of related genera, indicating that the database is sufficiently robust to support future studies, in which molecular identification of endophytes is made via analysis of ribosomal DNA sequences.

Alternaria toxins alternariol and alternariol monomethyl ether in grain foods in Canada

Alternaria alternata has been reported to be the most common fungus on Canadian Western wheat. The Alternaria toxins alternariol (AOH) and alternariol monomethyl ether (AME) are mutagenic in vitro and there is also limited evidence for carcinogenic properties. They have been found in wheat from Europe, Argentina, China and Australia, but they have not been looked for in Canadian grains or grain foods. In the present study, 83 samples of grain-based food sold in Canada, including flour, bran, breakfast cereals, infant cereals and bread, were analysed for AOH and AME using extraction with methanol, clean-up on combined aminopropyl/C18 solid phase extraction (SPE) columns, and liquid chromatography (LC) with tandem mass spectrometric (MS/MS) determination. The overall average recoveries of AOH and AME from a variety of spiked cereal foods (n = 13) were 45 ± 9% and 53 ± 9%, which could be attributed mainly to MS matrix effects The instrumental limits of detection (LOD) were 0.34 ng/g and 0.13 ng/g for AOH and AME, respectively, and the instrumental limits of quantitation (LOQ) were 1.1 and 0.43 ng/g. Of 83 samples analysed, 70 were positive for AOH (up to 63 ng/g, in a soft wheat bran) and 64 contained AME (up to 12 ng/g in a bran-based breakfast cereal). Of particular interest was the presence of AOH and/or AME in 27 out of 30 infant foods (up to 4.4 ng/g and 9.0 ng/g, respectively, in a sample of multigrain cereal).