Soybean Fungal Endophytes Alternaria and Diaporthe spp. are Differentially Impacted by Fungicide Application

Diversity and plant growth promotion potential of endophytic fungi isolated from hairy vetch in Japan

Hairy vetch (Vicia villosa Roth), a leguminous plant with nitrogen-fixing ability, is used as a cover crop and has the potential to suppress weeds and plant diseases. The microbial composition, particularly fungal endophytes, which may be related to the beneficial functions of this crop, has not been previously studied. In this study, we analyzed the diversity and function of culturable fungal endophytes associated with hairy vetch from eight locations across Japan. Using the fungal culture method, a total of 2,186 isolates were recovered and assigned to 80 distinct internal transcribed spacer (ITS) genotypes, spanning 28 genera. The results demonstrated that geographic location and soil physicochemical properties significantly influence the community composition of the hairy vetch fungal endophytes. Soil pH showed a significant positive correlation with the abundance of Penicillium, which was the most dominant genus in all the sampling locations and tissues. The majority of the isolates promoted plant growth and colonized hairy vetch and soybean roots, significantly promoting the growth of hairy vetch and/or soybean plants. Among the isolates, Penicillium griseofulvum AKL25 and Trichoderma koningii AKR15 significantly enhanced both hairy vetch and soybean growth, respectively. Meanwhile, Alternaria alternata OGL80 significantly increased soybean growth, but it did not affect hairy vetch growth, indicating host specificity of the fungal endophytes. In conclusion, this study showed that soil properties and geographic location play a critical role in shaping the community composition and structure of endophytic fungi associated with hairy vetch. Additionally, the isolated fungi promoted hairy vetch and soybean growth, with a host preference. Furthermore, this study revealed that a novel endophytic fungus, P. griseofulvum AKL25, which has high growth-promoting activity, can be utilized as a microbial inoculant to promote hairy vetch and soybean growth in sustainable agriculture.

Impact of Foliar Fungicide Application on the Culturable Fungal Endophyte Community of Soybean Seed in the Midwest United States

The purpose of our study was to determine whether the application of quinone outside inhibitor (QoI) and pyrazole-carboxamide fungicides as a tank mix would impact the endophyte community of soybean seed. Field trials during 2018 in Iowa, South Dakota, and Wisconsin, U.S.A., investigated the impact of a single combination fungicide spray at early pod set in soybeans. The composition of culturable endophytic fungi in mature soybean seed was assessed on three cultivars per state, with maturity groups (MGs) ranging from 1.1 to 4.7. An unusually wet 2018 season delayed harvest, which led to a high level of fungal growth in grain. The survey included 1,080 asymptomatic seeds that were disinfested and individually placed on 5-cm-diameter Petri plates of acidified water agar. The survey yielded 721 fungal isolates belonging to 24 putative species in seven genera; taxa were grouped into genera based on a combination of morphological and molecular evidence. The dominant genera encountered in the survey were Alternaria, Diaporthe, and Fusarium. The study showed that the fungicide treatment reduced the incidence of Fusarium in Wisconsin seed, increased the incidence of Diaporthe in seed from all states, and had no impact on the incidence of Alternaria. This is one of the first attempts to characterize the diversity of seed endophytes in soybean and the first to characterize the impacts of fungicide spraying on these endophyte communities across three states. Our study provides evidence that the impact of a fungicide spray on soybean seed endophyte communities may be influenced by site, weather, and cultivar maturity group.

Fungal Endophytes: Discovering What Lies within Some of Canada's Oldest and Most Resilient Grapevines

Plant diseases and pests reduce crop yields, accounting for global crop losses of 30% to 50%. In conventional agricultural production systems, these losses are typically controlled by applying chemical pesticides. However, public pressure is mounting to curtail agrochemical use. In this context, employing beneficial endophytic microorganisms is an increasingly attractive alternative to the use of conventional chemical pesticides in agriculture. A multitude of fungal endophytes are naturally present in plants, producing enzymes, small peptides, and secondary metabolites due to their bioactivity, which can protect hosts from pathogens, pests, and abiotic stresses. The use of beneficial endophytic microorganisms in agriculture is an increasingly attractive alternative to conventional pesticides. The aim of this study was to characterize fungal endophytes isolated from apparently healthy, feral wine grapes in eastern Canada that have grown without agrochemical inputs for decades. Host plants ranged from unknown seedlings to long-lost cultivars not widely propagated since the 1800s. HPLC-MS was used to identify unique endophyte-derived chemical compounds in the host plants, while dual-culture competition assays showed a range in endophytes' ability to suppress the mycelial growth of Botrytis, which is typically controlled in viticulture with pesticides. Twelve of the most promising fungal endophytes isolated were identified using multilocus sequencing and morphology, while DNA barcoding was employed to identify some of their host vines. These fungal endophyte isolates, which consisted of both known and putative novel strains, belonged to seven genera in six families and five orders of Ascomycota. Exploring the fungal endophytes in these specimens may yield clues to the vines' survival and lead to the discovery of novel biocontrol agents.

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.

Seed Treatment With Systemic Fungicides: Time for Review

Pre-sowing seed treatment with systemic fungicides is a firmly entrenched practice for most agricultural crops worldwide. The treatment is intended to protect the crop against seed- and soil-borne diseases. In recent years, there is increasing evidence that fungicidal applications to manage diseases might inadvertently also affect non-target organisms, such as endophytes. Endophytes are ubiquitously present in plants and contribute to plant growth and development besides offering resistance to biotic and abiotic stresses. In seeds, endophytes may play a role in seed development, seed germination, seedling establishment and crop performance. In this paper, we review the recent literature on non-target effects of fungicidal applications on endophytic fungal community and discuss the possible consequences of indiscriminate seed treatment with systemic fungicide on seed endophytes. It is now well recognized that endophytes are ubiquitously present in all parts of the plant, including the seeds. They may be transmitted vertically from seed to seed as in many grasses and/or acquired horizontally from the soil and the environment. Though the origins and evolution of these organisms in plants are a matter of conjecture, numerous studies have shown that they symbiotically aid in plant growth and development, in nutrient acquisition as well in protecting the plants from abiotic and biotic stresses. Against this background, it is reasonable to assume that the use of systemic fungicides in seed treatment may not only affect the seed endophytes but also their attendant benefits to seedling growth and establishment. While there is evidence to indicate that fungicidal applications to manage plant diseases also affect foliar endophytes, there are only few studies that have documented the effect of seed treatment on seed-borne endophytes. Some of the convincing examples of the latter come from studies on the effect of fungicide application on rye grass seed endophyte AR37. More recently, experiments have shown that removal of seed endophytes by treatment with systemic fungicides leads to significant loss of seedling vigour and that such losses could be partially restored by enriching the seedlings with the lost endophytes. Put together, these studies reinforce the importance of seed endophytes to seedling growth and establishment and draw attention on how to trade the balance between the benefits of seed treatments and the direct and indirect costs incurred due to loss of endophytes. Among several approaches, use of reduced-risk fungicides and identifying fungicide-resistant endophytes are suggested to sustain the endophyte contribution to early seedling growth.

Real-Time PCR Assay for the Diagnosis and Quantification of Co-infections by Diaporthe batatas and Diaporthe destruens in Sweet Potato

Foot rot disease caused by Diaporthe destruens (formerly Plenodomus destruens) has become a major concern for the production of sweet potato [Ipomoea batatas (L.) Lam.] in Japan. A related fungus Diaporthe batatas, which causes dry rot disease of sweet potato, is native and is widespread in fields in Japan. The similar characteristics of these two pathogens pose a challenge for conventional disease diagnosis. Currently, there are no effective molecular measures for identifying and distinguishing D. destruens and D. batatas. Here, we demonstrate a real-time PCR assay that distinguishes and quantifies D. batatas and D. destruens from co-infected sweet potato. The assay was performed with various simulated DNA combinations of D. batatas and D. destruens ranging from 1:1 to 1:100000. The assay was also used with the ratios of D. batatas: D. destruens: sweet potato DNA ranging from 1:1:1 to 1:1:100000. These assays produced a specific amplification product for each of the pathogens, and quantified the fungal biomass over the entire range tested without detecting false positives. The assay was validated by using infected sweet potato collected from various fields; it showed sufficient sensitivity and specificity to quantify and distinguish D. batatas and D. destruens from these field samples. Thus, our real-time PCR assay would be a useful tool for diagnosis of D. batatas and D. destruens and is expected to provide the foundation for the design of integrated disease management strategies for foot rot disease in sweet potato.

Diaporthe Seed Decay of Soybean [Glycine max (L.) Merr.] Is Endemic in the United States, But New Fungi Are Involved

Diaporthe seed decay can compromise seed quality in soybean [Glycine max (L.) Merr.] in the warm and humid production areas of the United States during crop maturation. In the current study, 45 isolates of Diaporthe were recovered from seed sampled from soybean fields affected by Diaporthe-associated diseases in eight U.S. states in 2017. The isolates obtained belonged to 10 species of Diaporthe based on morphology and phylogenetic analyses of the internal transcribed spacer, partial translation elongation factor 1-α, and β-tubulin gene sequences. The associated species included D. aspalathi, D. caulivora, D. kongii, D. longicolla, D. sojae, D. ueckerae, D. unshiuensis, and three novel fungi, D. bacilloides, D. flavescens, and D. insulistroma. One isolate each of the 10 species was examined for pathogenicity on seed of cultivar Sava under controlled conditions. Seven days postinoculation, significant differences in the percentages of decayed seeds and seedling necrosis were observed among the isolates and the noninoculated control (P < 0.0001). While the isolates of D. bacilloides, D. longicolla, and D. ueckerae caused a significantly greater percentage of decayed seeds (P < 0.0001), the isolate of D. aspalathi caused the greatest seedling necrosis (P < 0.0001). The observation of new fungi causing Diaporthe seed decay suggests the need for a more comprehensive survey in U.S. soybean producing areas since members of the genus Diaporthe appear to form a complex that causes seed decay.

Effects of Soybean Cultivar, Foliar Application of Azoxystrobin, and Year on Seed Vigor and Microflora Under Delayed Harvest Conditions

The effects of cultivar and foliar fungicide applications on soybean seed germination, vigor, microflora, and yield after delayed harvest were determined at the University of Arkansas Vegetable Research Station in Kibler, AR, from 2008 to 2010. Seven cultivars with varying levels of resistance to Diaporthe spp. or Cercospora spp. were treated or not treated with a foliar application of azoxystrobin at the R5 growth stage. Plots were harvested 3 weeks after the plants had reached harvest maturity. Yields were recorded, samples of seed were collected, and standard germination (SG) and accelerated aging (AA) were assessed. Seeds were also assayed for infection by fungi on modified potato dextrose agar and by bacteria on nutrient agar. Seed vigor was significantly reduced by infection with Diaporthe spp., Fusarium spp., and Bacillus subtilis, but not with Cercospora spp. Cultivar had a significant impact on yield, seed vigor, and seed infection levels. The cultivar Osage had consistently high seed vigor and low overall seed infection incidence throughout the study. MO/PSD-0259, AG 4403, and UA 4805 also had relatively high seed vigor and low seed infection rates. PI 80837 had a low incidence of seed infection by Diaporthe spp. and Fusarium spp. in 2008 and 2010, but high levels in 2009, when environmental conditions were especially favorable for these pathogens. AP 350 and Suweon97 had relatively high seed infection incidences, particularly of Diaporthe spp. and Fusarium spp., and relatively low seed vigor. Application of the foliar fungicide azoxystrobin at the R5 growth stage significantly increased AA across years and cultivars and increased seed infection by Diaporthe spp. in 2009 across cultivars. There were significant negative correlations between yield and seed infection by Diaporthe spp. and Bacillus subtilis during 1 year and with Fusarium spp. during all 3 years. Overall, resistance to seed infection can persist even when harvest is delayed. In addition to Diaporthe spp., other seedborne pathogens may reduce seed vigor and yield.

Soybean anthracnose caused by Colletotrichum species: Current status and future prospects

Soybean (Glycine max) is one of the most important cultivated plants worldwide as a source of protein-rich foods and animal feeds. Anthracnose, caused by different lineages of the hemibiotrophic fungus Colletotrichum, is one of the main limiting factors to soybean production. Losses due to anthracnose have been neglected, but their impact may threaten up to 50% of the grain production.

TAXONOMY

While C. truncatum is considered the main species associated with soybean anthracnose, recently other species have been reported as pathogenic on this host. Until now, it has not been clear whether the association of new Colletotrichum species with the disease is related to emerging species or whether it is due to the undergoing changes in the taxonomy of the genus.

DISEASE SYMPTOMS

Typical anthracnose symptoms are pre- and postemergence damping-off; dark, depressed, and irregular spots on cotyledons, stems, petioles, and pods; and necrotic laminar veins on leaves that can result in premature defoliation. Symptoms may evolve to pod rot, immature opening of pods, and premature germination of grains.

CHALLENGES

As accurate species identification of the causal agent is decisive for disease control and prevention, in this work we review the taxonomic designation of Colletotrichum isolated from soybean to understand which lineages are pathogenic on this host. We also present a comprehensive literature review of soybean anthracnose, focusing on distribution, symptomatology, epidemiology, disease management, identification, and diagnosis. We consider the knowledge emerging from population studies and comparative genomics of Colletotrichum spp. associated with soybean providing future perspectives in the identification of molecular factors involved in the pathogenicity process.

USEFUL WEBSITE

Updates on Colletotrichum can be found at http://www.colletotrichum.org/. All available Colletotrichum genomes on GenBank can be viewed at http://www.colletotrichum.org/genomics/.