Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

Evaluation of the rhizospheric microbiome of the native colonizer Piptatherum miliaceum in semiarid mine tailings

The study of the rhizospheric microbiome in native plants should be a prerequisite before carrying out the phytomanagement of mine tailings. The goal of this work was to evaluate the rhizospheric microbiome of Piptatherum miliaceum in semiarid mine tailings. A comprehensive edaphic characterization was performed including the description of soil microbial composition in the rhizosphere of P. miliaceum growing at a mine tailings pile and at a control site. Plant nutritional and isotopic compositions were also determined. Neutral pH of the tailings (7.3) determined low metal extractability in 0.01 M CaCl2 (e.g. < 1 mg/kg for Zn). In spite of the contrasting edaphic fertility conditions of both sites, N (~ 15 g kg-1) and P (~ 400 mg kg-1) leaf concentrations were similar. The lower δ15N at the tailings plants (- 4.50‰) compared to the control (6.42‰) indicated greater efficiency of P. miliaceum for uptaking N under the low fertility conditions of the tailings (0.1% total soil nitrogen). The presence at the tailings of bacterial orders related to the cycling of N, such as Rhizobiales, could have contributed to enhance N acquisition. The lower leaf δ13C values at the tailings (- 30.22‰) compared to the control (- 28.47‰) indicated lower water use efficiency of the tailing plants. Some organotrophic bacterial and fungal groups in the tailings' rhizospheres were also found in the control site (e.g. Cytophagales, Sphingobacteriales for bacteria; Hypocreales, Pleosporales for fungi). This may indicate that P. miliaceum is able to shape its own specific microbiome at the tailings independently from the initial microbial composition of the tailings.

Establishment of Beauveria bassiana as a fungal endophyte in potato plants and its virulence against potato tuber moth, Phthorimaea operculella (Lepidoptera: Gelechiidae)

The potato tuber moth, Phthorimaea operculella, is the most damaging potato pest in the world and is difficult to control as the larvae are internal feeders in the foliage and tubers. Entomopathogenic fungi that colonize plants as endophytes have lethal and sublethal pathological effects on insect pests. We show that Beauveria bassiana colonizes the aerial parts of potato plants endophytically after inoculation through soil drenching. Endophytic B. bassiana persisted in potato foliage for more than 50 days postinoculation. Bioassays indicated that foliage of B. bassiana-inoculated potato plants were pathogenic against larvae of P. operculella. Sublethal experiments indicated that B. bassiana negatively affected the growth, development, and reproduction of P. operculella. Development experiments showed that the weight of P. operculella pupae reared on B. bassiana-colonized potato plants (4.25 mg) was significantly less than that of those reared on uninoculated control plants (8.89 mg). Compared with newly eclosed larvae fed on control plants, those fed on B. bassiana-inoculated plants had significantly lower survivorship, with only 17.8% developing to the adult stage. Oviposition of P. operculella females reared on B. bassiana endophytically colonized plants was significantly lower (35 eggs/female) than of those reared on uninoculated plants (115 eggs/female). This study demonstrates that endophytic B. bassiana can be a potential biological control agent for the control and management of P. operculella. Comparing pupal weights of P. operculella reared on potato plants inoculated with the B. bassiana strain GZGY-1-3 and on untreated control plants, pupae from the control plants were significantly heavier than those from treated plants.

Three Methods Assessing the Association of the Endophytic Entomopathogenic Fungus Metarhizium robertsii with Non-Grafted Grapevine Vitis vinifera

Characterizing the association of endophytic insect pathogenic fungi (EIPF) with plants is an important step in order to understand their ecology before using them in biological control programs. Since several methods are available, it is challenging to identify the most appropriate for such investigations. Here, we used two strains of Metarhizium robertsii: EF3.5(2) native to the French vineyard environment and ARSEF-2575-GFP a laboratory strain expressing a green fluorescent protein, to compare their potential of association with non-grafted grapevine Vitis vinifera. Three methods were used to evaluate the kinetics of rhizosphere and grapevine endospheric colonization: (i) Droplet Digital (ddPCR), a sensitive molecular method of M. robertsii DNA quantification in different plant parts, (ii) culture-based method to detect the live fungal propagules from plant tissues that grew on the medium, (iii) confocal imaging to observe roots segments. Both strains showed evidence of establishment in the rhizosphere of grapevines according to the culture-based and ddPCR methods, with a significantly higher establishment of strain EF3.5(2) (40% positive plants and quantified median of exp(4.61) c/μL) compared to strain ARSEF-2575-GFP (13% positive plants and quantified median of exp(2.25) c/μL) at 96-98 days post-inoculation. A low incidence of association of both strains in the grapevine root endosphere was found with no significant differences between strains and evaluation methods (15% positive plants inoculated with strain EF3.5(2) and 5% with strain ARSEF-2575-GFP according to culture-based method). ddPCR should be used more extensively to investigate the association between plants and EIPF but always accompanied with at least one method such as culture-based method or confocal microscopy.

Isolation and identification of two Beauveria bassiana strains from silkworm, Bombyx mori

Silkworm diseases caused by fungi infection occur frequently in sericulture and brought huge economic loss to sericulture. However, on the other hand, some fungi such as Beauveria bassiana, as an important entomological fungus, play an important role in biological control of insect pests. Here, two fungal pathogens causing yellow muscardine were isolated from the silkworm and named as SZY1 and SZY2. These two strains showed almost the same conidial morphology which were smooth, near-spherical, spherical, or ovoid and 2.7 ± 0.6 µm × 2.5 ± 0.9 µm in size, and the hyphal growth rate was also similar. However, the conidia production of SZY2 was almost twice as many as that of SZY1. The complete ribosomal RNA gene was sequenced and analyzed. As a result, the gene sequences of internal transcript space 1 (ITS1)-5.8S rRNA-internal transcript space 2 (ITS2) of SZY1 and SZY2 were identical in sequence and size, and for 18S rRNA, 28S rRNA, and intergenic spacer (IGS), the gene identity of SZY1 to SZY2 was 99%, 99%, and 98%, respectively. Results of phylogenetic analysis based on either ITS1-5.8S rRNA-ITS2 or 18S rRNA showed that both SZY1 and SZY2 were closely related to Beauveria bassiana. These results revealed that the pathogens of yellow muscardine SZY1 and SZY2 were identified as two different strains of Beauveria bassiana, which could provide diagnostic evidence for silkworm muscardine and was helpful for the research and development of novel Bombyx batryticatus and fungal biological insecticide.

Characterization of cadmium-tolerant endophytic fungi isolated from soybean (Glycine max) and barley (Hordeum vulgare)

Cadmium stress disrupts plant-microbial interactions and reduces plant growth and development. In plants, the tolerance to stress can be increased by inoculation with endophytic microorganisms. The aim of this study was to investigate the distribution of endophytic fungi in various plant organs of barley and soybean and evaluate their Cd removal ability. Two hundred fifty-three fungal strains were isolated from various organs of barley (Hordeum vulgare cv Arna) and soybean (Glycine max cv Almaty). The colonization rate ranged from 13.6% to 57.3% and was significantly higher in the roots. Ten genera were identified: Fusarium, Penicillium, Aspergillus, Metarhizium, Beauveria, Trichoderma, Rhodotorula, Cryptococcus, Aureobasidium and Metschnikowia. Twenty-three fungal strains have a Cd tolerance index from 0.24 to 1.12. Five strains (Beauveria bassiana T7, Beauveria bassiana T15, Rhodotorula mucilaginosa MK1, Rhodotorula mucilaginosa RH2, Metschnikowia pulcherrima MP2) with the highest level of Cd tolerance have minimum inhibitory concentrations from 290 to 2400 μg/ml. These fungi were able to remove Cd up to 59%. The bioaccumulation capacity ranged from 2.3 to 11.9 mg/g. Selected fungal strains could be considered as biological agents for their potential application in the bioremediation of contaminated sites.

Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

Pest management via endophytic colonization of tobacco seedlings by the insect fungal pathogen Beauveria bassiana

BACKGROUND

It has been suggested that entomopathogenic fungi can be introduced into plants as endophytes potentially leading to insect control. Here, we sought to identify specific strains of the insect pathogenic fungus, Beauveria bassiana that would form endophytic associations with tobacco (Nicotiana benthamiana) benefitting host plant growth and/or resistance against insect pests and pathogens.

RESULTS

Tobacco seeds were inoculated with six different B. bassiana strains and entophytic colonization, plant growth, and resistance to pathogens and insect pests were evaluated over a 50 day-period. Although all the strains could colonize seedlings, 90% seedling colonization was seen for four strains. Fungal cells could be detected in stems more readily than in leaf and root tissues. Colonization by B. bassiana boosted plant growth with an increased photosynthetic rate, chlorophyll content, and stomatal and trichome density seen in fungal treated plants. Tobacco seedlings colonized by specific B. bassiana strains displayed significantly increased tolerance/resistance against bacterial and fungal pathogens. B. bassiana-colonized seedlings also displayed higher resistance to aphids (Myzus persicae) as compared to untreated controls. Colonization by B. bassiana was shown to trigger both of the salicylic acid (SA) and jasmonate acid (JA) defense pathways, but SA pathway was upregulated much more than JA pathway for some of the tested strains.

CONCLUSION

Specific strains of B. bassiana can be introduced into host plants as endophytes, resulting in promotion of host plant growth, increased resistance to microbial pathogens, and/or increased resistance to insect pests. © 2020 Society of Chemical Industry.

Root fungal endophytes: identity, phylogeny and roles in plant tolerance to metal stress

Metal trace elements accumulate in soils mainly because of anthropic activities, leading living organisms to develop strategies to handle metal toxicity. Plants often associate with root endophytic fungi, including nonmycorrhizal fungi, and some of these organisms are associated with metal tolerance. The lack of synthetic analyses of plant-endophyte-metal tripartite systems and the scant consideration for taxonomy led to this review aiming (1) to inventory non-mycorrhizal root fungal endophytes described with respect to their taxonomic diversity and (2) to determine the mutualistic roles of these plant-fungus associations under metal stress. More than 1500 species in 100 orders (mainly Hypocreales and Pleosporales) were reported from a wide variety of environments and hosts. Most reported endophytes had a positive effect on their host under metal stress, but with various effects on metal uptake or translocation and no clear taxonomic consistency. Future research considering the functional patterns and dynamics of these associations is thus encouraged.

Edaphic factors determining the colonization of semiarid mine tailings by a ruderal shrub and two tree plant species: Implications for phytomanagement

Phytomanagement has been considered a feasible technique to decrease the environmental risks associated to mine tailings and its implementation relies on a suitable plant species selection. The goal of this study was to identify the edaphic factors, including microbiology, affecting the establishment of plant species with contrasting growth patterns during the phytomanagement of mine tailings. For this purpose, a comprehensive rhizosphere characterization was performed in an early ruderal colonizer, Zygophyllum fabago and two late successional tree species, Pinus halepensis and Tetraclinis articulata, growing at a mine tailings pile in southeast Spain. The neutral pH of the tailings determined low 0.01 M CaCl₂ metal extractable concentrations (e.g. <10 μg kg^-1 Pb and Cd). Thus, other soil properties different from metal concentrations resulted more determining to explain plant establishment. Results revealed that Z. fabago selectively colonized tailings patches characterized by high salinity (3.5 dS m^-1) and high silt percentages (42%), showing a specific halotolerant rhizospheric microbial composition, such as the bacterial Sphingomonadales and Cytophagales orders and the fungal Pleosporales and Hyprocreales orders. The two tree species grew at moderate salinity areas of the tailings pile (1.7 dS m^-1) with high sand percentages (85%), where Actinomycetales was the most abundant bacterial order (>10% abundance). The contrasting mycorrhizal behaviour of both tree species (ectomycorrhizal for P. halepensis and endomycorrhizal for T. articulata) could explain the differences found between their fungal rhizospheric composition. In terms of phytomanagement, the selective plant species colonization following specific soil patches at mine tailings would increase their biodiversity and resilience against environmental stressors.

Entomopathogenic Fungi as Endophytes for Biological Control of Subterranean Termite Pests Attacking Cocoa Seedlings

This study was conducted in the scope of developing a sustainable effective approach against subterranean termite pests using entomopathogenic and endophytic fungus-based biopesticides. Termites, Odontotermes spp. workers, were tested for their susceptibility to 15 entomopathogenic fungal isolates through the direct spraying of conidia suspensions at 1 × 108 conidia/mL. In general, all the isolates screened were pathogenic, with 100% mortality 4-7 days post-inoculation. However, the most virulent isolates were Metarhizium brunneum Cb15-III; the M. anisopliae isolates ICIPE 30 and ICIPE 60; Hypocrea lixii F3ST1; and the Beauveria bassiana isolates ICIPE 279, ICIPE 706 and ICIPE 662. These isolates were further tested for their endophytic colonization of cocoa seedlings using seed soaking, soil drench and foliar spray at 1 × 108 conidia/mL. The colonization of the plant tissues by the fungi was determined using a culture-based technique. Only the B. bassiana isolates ICIPE 706 and ICIPE 279, and H. lixii F3ST1 colonized the cocoa seedlings, with varied colonization rates among isolates and inoculation methods. Three naturally occurring endophytes-Trichoderma asperellum, Fusarium solani and F. redolens-were also isolated from the cocoa seedling tissues. These findings suggest that cocoa seedlings are conducive to endophytic fungal growth either occurring naturally or from artificial inoculation Our findings could possibly lead to an innovative approach to the management of herbivory and subterranean termite pests in cocoa agroforests.

From Concept to Commerce: Developing a Successful Fungal Endophyte Inoculant for Agricultural Crops

The development of endophyte inoculants for agricultural crops has been bedevilled by the twin problems of a lack of reliability and consistency, with a consequent lack of belief among end users in the efficacy of such treatments. We have developed a successful research pipeline for the production of a reliable, consistent and environmentally targeted fungal endophyte seed-delivered inoculant for barley cultivars. Our approach was developed de novo from an initial concept to source candidate endophyte inoculants from a wild relative of barley, Hordeum murinum (wall barley). A careful screening and selection procedure and extensive controlled environment testing of fungal endophyte strains, followed by multi-year field trials has resulted in the validation of an endophyte consortium suitable for barley crops grown on relatively dry sites. Our approach can be adapted for any crop or environment, provided that the set of first principles we have developed is followed. Here, we report how we developed the successful pipeline for the production of an economically viable fungal endophyte inoculant for barley cultivars.

Beauveria bassiana and Metarhizium anisopliae endophytically colonize cassava roots following soil drench inoculation

We investigated the fungal entomopathogens Beauveria bassiana and Metarhizium anisopliae to determine if endophytic colonization could be achieved in cassava. An inoculation method based on drenching the soil around cassava stem cuttings using conidial suspensions resulted in endophytic colonization of cassava roots by both entomopathogens, though neither was found in the leaves or stems of the treated cassava plants. Both fungal entomopathogens were detected more often in the proximal end of the root than in the distal end. Colonization levels of B. bassiana were higher when plants were sampled at 7-9 days post-inoculation (84%) compared to 47-49 days post-inoculation (40%). In contrast, the colonization levels of M. anisopliae remained constant from 7-9 days post-inoculation (80%) to 47-49 days post-inoculation (80%), which suggests M. anisopliae is better able to persist in the soil, or as an endophyte in cassava roots over time. Differences in colonization success and plant growth were found among the fungal entomopathogen treatments.