Impact of three different fungicides on fungal epi- and endophytic communities of common bean (Phaseolus vulgaris) and broad bean (Vicia faba)

Proposal of one new family, seven new genera and seventy new basidiomycetous yeast species mostly isolated from Tibet and Yunnan provinces, China

More than 2 000 yeast strains isolated from 1 200 samples mostly collected from Tibet and Yunnan provinces in China were identified as 462 species according to the internal transcribed spacer including the 5.8S rDNA (ITS) and the D1/D2 domains of the large subunit rDNA (LSU) sequence analyses. Among them, 70 new basidiomycetous yeast species were proposed based on the multi-locus phylogenetic analyses including the D1/D2 domains, the ITS, the small subunit rDNA (SSU), the largest subunit of RNA polymerase II (RPB1), the second largest subunit of RNA polymerase II (RPB2) and translation elongation factor 1-α (TEF1), as well as the phenotypic comparisons. The average nucleotide identity (ANI) analysis with the genomic metric was also used in the evaluation of the species delimitation for the genera Holtermannia, Mrakia and Takashimella that contain closely related species with low sequence heterogeneity in both ITS and D1/D2 regions. Forty-six new species belonged to 16 genera in the Agaricomycotina, 13 new species occurred in 12 genera in the Pucciniomycotina, three new species were distributed in three genera in the Ustilaginomycotina, and eight new species were classified in seven newly established genera. One new family was also proposed based on one of these new genera. The analyses revealed several inaccurate species names attributed to genomes deposited in GenBank, indicating the necessity of a more rigorous quality checks of the genomes deposited in the public databases. Taxonomic novelties: New family: Vankyiozymaceae Q.-M. Wang; New genera: Baiomyces Q.-M. Wang, Bauerozyma Q.-M. Wang, Fengyania Q.-M. Wang, Foliozyma Q.-M. Wang, Litoriozyma Q.-M. Wang, Nakaseozyma Q.-M. Wang, Vankyiozyma Q.-M. Wang; New species: Baiomyces sejilaensis Q.-M. Wang, Bauerozyma artemisiae Q.-M. Wang, Boekhoutia foliicola Q.-M. Wang, Buckleyzyma pseudoaurantiaca Q.-M. Wang, Carlosrosaea betulae Q.-M. Wang, Carlosrosaea rhododendri Q.-M. Wang, Carlosrosaea yunnanensis Q.-M. Wang, Chrysozyma quercicola Q.-M. Wang, Curvibasidium pini Q.-M. Wang, Cystobasidium cunninghamiae Q.-M. Wang, Derxomyces foliicola Q.-M. Wang, Derxomyces motuoensis Q.-M. Wang, Derxomyces orientalis Q.-M. Wang, Derxomyces paracylindricus Q.-M. Wang, Exobasidium lijiangense Q.-M. Wang, Fengyania pteridophytorum Q.-M. Wang, Foliozyma liliicola Q.-M. Wang, Halobasidium phyllophilum Q.-M. Wang, Hannaella artemisiae Q.-M. Wang, Hannaella pteridophytorum Q.-M. Wang, Hannaella urticae Q.-M. Wang, Holtermannia pseudosaccardoi Q.-M. Wang, Kockovaella cariosiligni Q.-M. Wang, Kockovaella foliicola Q.-M. Wang, Kondoa tibetensis Q.-M. Wang, Kwoniella hippophaes Q.-M. Wang, Kwoniella lonicerae Q.-M. Wang, Litoriozyma hainanensis Q.-M. Wang, Meira marina Q.-M. Wang, Microsporomyces betulae Q.-M. Wang, Microsporomyces foliicola Q.-M. Wang, Mrakia pini Q.-M. Wang, Mrakia rhododendri Q.-M. Wang, Nakaseozyma junci Q.-M.Wang, Nakaseozyma lonicerae Q.-M. Wang, Papiliotrema castaneae Q.-M. Wang, Papiliotrema catalpae Q.-M. Wang, Phaeotremella pini Q.-M. Wang, Phaffia paratasmanica Q.-M. Wang, Phaffia rhododendri Q.-M. Wang, Piskurozyma cuscutae Q.-M. Wang, Piskurozyma humicola Q.-M. Wang, Piskurozyma liliaceifoliae Q.-M. Wang, Piskurozyma linzhiensis Q.-M. Wang, Piskurozyma nanyiensis Q.-M. Wang, Piskurozyma terricola Q.-M. Wang, Pseudohyphozyma sanghuangpori Q.-M. Wang, Pseudotremella hippophaes Q.-M. Wang, Pseudotremella rhododendri Q.-M. Wang, Rhodotorula linzhiensis Q.-M. Wang, Slooffia terricola Q.-M. Wang, Takashimella corticis Q.-M. Wang, Teunia betulicola Q.-M. Wang, Teunia chimonanthi Q.-M. Wang, Teunia heritierae Q.-M. Wang, Teunia myricariae Q.-M. Wang, Teunia parabetulicola Q.-M. Wang, Teunia quercus Q.-M. Wang, Teunia rhododendri Q.-M. Wang, Ustilago foliicola Q.-M. Wang, Vankyiozyma motuoensis Q.-M. Wang, Vanrija silvicola Q.-M. Wang, Vishniacozyma catalpae Q.-M. Wang, Vishniacozyma marinae Q.-M. Wang, Vishniacozyma paravictoriae Q.-M. Wang, Vishniacozyma pini Q.-M. Wang, Vishniacozyma pyri Q.-M. Wang, Vishniacozyma sinopodophylli Q.-M. Wang, Vishniacozyma zhenxiongensis Q.-M. Wang, Yurkovia castaneae Q.-M. Wang. Citation: Jiang Y-L, Bao W-J, Liu F, Wang G-S, Yurkov AM, Ma Q, Hu Z-D, Chen X-H, Zhao W-N, Li A-H, Wang Q-M (2024). Proposal of one new family, seven new genera and seventy new basidiomycetous yeast species mostly isolated from Tibet and Yunnan provinces, China. Studies in Mycology 109: 57-153. doi: 10.3114/sim.2024.109.02.

Comparative Analysis of Rhizosphere and Endosphere Fungal Communities in Healthy and Diseased Faba Bean Plants

This study used the ITS approach based on Illumina MiSeq sequencing to assess the endosphere and rhizosphere fungal communities in healthy and diseased faba bean plants. The findings indicate that the most predominant phyla in all samples were Ascomycota (49.89-99.56%) and Basidiomycota (0.33-25.78%). In healthy endosphere samples, Glomeromycota (0.08-1.17%) was the only predominant phylum. In diseased endosphere samples, Olpidiomycota (0.04-1.75%) was the only predominant phylum. At the genus level, Penicillium (0.47-35.21%) was more abundant in rhizosphere soil, while Paraphoma (3.48-91.16%) was predominant in the endosphere roots of faba bean plants. Significant differences were observed in the alpha diversity of rhizosphere samples from different germplasm resources (p < 0.05). The fungal community structures were clearly distinguished between rhizosphere and endosphere samples and between healthy and diseased endosphere samples (p < 0.05). Saccharomyces was significantly enriched in diseased endosphere samples, whereas Apiotrichum was enriched in healthy endosphere samples. Vishniacozyma and Phialophora were enriched in diseased rhizosphere samples, while Pseudogymnoascus was enriched in healthy rhizosphere samples. Diseased samples displayed more strongly correlated genera than healthy samples. Saprotrophs accounted for a larger proportion of the fungal microbes in rhizosphere soil than in endosphere roots. This study provides a better understanding of the composition and diversity of fungal communities in the rhizosphere and endosphere of faba bean plants as well as a theoretical guidance for future research on the prevention or control of faba bean root rot disease.

Changes in the Endophytic Bacterial Community of Brassica rapa after Application of Systemic Insecticides

Insecticides not only control target pests but also adversely affect non-target communities including humans, animals, and microbial communities in host plants and soils. The effect of insecticides on non-target communities, especially endophytic bacterial communities, remains poorly understood. Two phases of treatments were conducted to compare the trends in endophytic bacterial response after insecticide application. Endophytic bacteria were isolated at 2 and 4 weeks after germination. Most insecticide treatments showed a declining trend in bacterial diversity and abundance, whereas an increasing trend was observed in the control. Therefore, insecticide use negatively affected non-target endophytic bacterial communities. Bacillus spp. was mostly dominant in the early stage in both insecticide treatment and control groups. Nevertheless, in the matured stage, mostly bacteria including Pseudomonas spp., Priestia spp. were dominant in groups treated with high insecticide concentrations. Therefore, plants can regulate and moderate their microbiome during their lifecycle depending on surrounding environmental conditions.

Influence of Geographical Orchard Location on the Microbiome from the Progeny of a Pecan Controlled Cross

Carya&amp;nbsp;illinoinensis (Wangenh.) K.Koch production has expanded beyond the native distribution as the genetic diversity of the species, in part, has allowed the trees to grow under broad geographic and climatic ranges. Research in other plant species has demonstrated that the phytobiome enhances their ability to survive and thrive in specific environments and, conversely, is influenced by the prevailing environment and plant genetics, among other factors. We sought to analyze the microbiota of pecan seedlings from the controlled cross 'Lakota' × 'Oaxaca' that were made in Georgia and Texas, respectively, to determine if the maternal geographical origin influences the microbiome of the resulting progeny. No significant differences in bacterial communities were observed between the seeds obtained from the two different states (p = 0.081). However, seed origin did induce significant differences in leaf fungal composition (p = 0.012). Results suggest that, in addition to some environmental, epigenetics, or host genetic components, ecological processes, such as dispersal mechanisms of the host, differentially impact the pecan microbiome, which may have ramifications for the health of trees grown in different environments. Future studies on the role of the microbiome in plant health and productivity will aid in the development of sustainable agriculture for improved food security.

An Insight into the Endophytic Bacterial Community of Tomato after Spray Application of Propiconazole and Bacillus subtilis Strain NBRI-W9

Propiconazole (PCZ) is a commonly sprayed fungicide against fungal pathogens. Being systemic in action, it reaches subcellular layers and impacts the endophytes. Although PCZ is a fungicide, it is hypothesized to exert an inhibitory effect on the bacterial endophytes. Therefore, this study aims to get an insight into the perturbations caused by the systemically acting antifungal agents PCZ and Bacillus subtilis (W9) and the consequences thereof. The current study compared the 16S rRNA microbial diversity, abundance, and functions of the endophytic bacterial community of tomato in response to PCZ, W9, and PCZ+W9 application. The implications of these treatments on the development of bacterial speck disease by Pseudomonas syringae were also studied. The culturable endophyte population fluctuated after (bio)fungicide application and stabilized by 72 h. At 72 h, the endophyte population was ~3.6 × 103 CFUg-1 in control and ~3.6 × 104 in W9, ~3.0 × 102 in PCZ, and ~5.3 × 103 in PCZ+W9 treatment. A bacterial community analysis showed a higher relative abundance of Bacillales, Burkholderiales, Rhizobiales, Pseudomonadales, and Actinomycetales in the W9 treatment compared with that in the PCZ treatment and control. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis showed enhanced metabolic pathways related to secretion, stress, chemotaxis, and mineral nutrition in the W9 treatment. Disease severity was greater in PCZ than that in the W9 treatment. Disease severity on tomato plants showed strong negative correlations with Sphingomonas (r = -0.860) and Janthinobacterium (r = -0.810), indicating that the natural biocontrol communities are agents of plant resistance to diseases. Outcomes show that systemic chemicals are a potential threat to the nontarget endophytes and that plants became susceptible to disease on endophyte decline; this issue could be overcome by the application of microbial inoculums. IMPORTANCE Endophytes are plant inhabitants acting as its extended genome. The present study highlights the importance of maintaining plant endophytes for sustainable disease resistance in plants. The impact of chemical fungicides and biofungicides was shown on tomato endophytes, in addition to their implications on plant susceptibility to bacterial speck disease. The observations point toward the deleterious effects of systemic pesticide application on endophyte niches that disrupt their diversity and functions compromising plant immunity.

The immunity priming effect of the Arabidopsis phyllosphere resident yeast Protomyces arabidopsidicola strain C29

The phyllosphere is a complex habitat for diverse microbial communities. Under natural conditions, multiple interactions occur between host plants and phyllosphere resident microbes, such as bacteria, oomycetes, and fungi. Our understanding of plant associated yeasts and yeast-like fungi lags behind other classes of plant-associated microbes, largely due to a lack of yeasts associated with the model plant Arabidopsis, which could be used in experimental model systems. The yeast-like fungal species Protomyces arabidopsidicola was previously isolated from the phyllosphere of healthy wild-growing Arabidopsis, identified, and characterized. Here we explore the interaction of P. arabidopsidicola with Arabidopsis and found P. arabidopsidicola strain C29 was not pathogenic on Arabidopsis, but was able to survive in its phyllosphere environment both in controlled environment chambers in the lab and under natural field conditions. Most importantly, P. arabidopsidicola exhibited an immune priming effect on Arabidopsis, which showed enhanced disease resistance when subsequently infected with the fungal pathogen Botrytis cinerea. Activation of the mitogen-activated protein kinases (MAPK), camalexin, salicylic acid, and jasmonic acid signaling pathways, but not the auxin-signaling pathway, was associated with this priming effect, as evidenced by MAPK3/MAPK6 activation and defense marker expression. These findings demonstrate Arabidopsis immune defense priming by the naturally occurring phyllosphere resident yeast species, P. arabidopsidicola, and contribute to establishing a new interaction system for probing the genetics of Arabidopsis immunity induced by resident yeast-like fungi.

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.

A novel Arabidopsis phyllosphere resident Protomyces species and a re-examination of genus Protomyces based on genome sequence data

Protomyces is an understudied genus of yeast-like fungi currently defined as phytopathogens of only Umbelliferae and Compositae. Species relationships and boundaries remain controversial and molecular data are lacking. Of the 82 named Protomyces, we found few recent studies and six available cultures. We previously isolated Protomyces strains from wild Arabidopsis thaliana, a member of Brassicaceae, a family distant from accepted Protomyces hosts. We previously sequenced the genomes of all available Protomyces species, and P. arabidopsidicola sp. nov. strain C29, from Arabidopsis. Phylogenomics suggests this new species occupied a unique position in the genus. Genomic, morphological, and physiological characteristics distinguished P. arabidopsidicola sp. nov. from other Protomyces. Nuclear gene phylogenetic marker analysis suggests actin1 gene DNA sequences could be used with nuclear ribosomal DNA internal transcribed spacer sequences for rapid identification of Protomyces species. Previous studies demonstrated P. arabidopsidicola sp. nov. could persist on the Arabidopsis phyllosphere and Protomyces sequences were discovered on Arabidopsis at multiple sites in different countries. We conclude that the strain C29 represents a novel Protomyces species and propose the name of P. arabidopsidicola sp. nov. Consequently, we propose that Protomyces is not strictly associated only with the previously recognized host plants.

Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species

Nearly 500 basidiomycetous yeast species were accepted in the latest edition of The Yeasts: A Taxonomic Study published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the Tremellomycetes (Agaricomycotina). The other 61 are distributed in 26 genera in the Pucciniomycotina. Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.

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

In field trials in Iowa, we investigated the association of a fungicide applied at early pod set to the diversity and composition of foliar endophytic fungi in presenescent soybeans. The main purpose of our study was to determine whether fungicides affect the microbiome of soybean plants during the pod-fill reproductive stage. In a replicated experiment focused on the impact of a fungicide application including a quinone outside inhibitor (QoI) and a pyrazole-carboxamide spanning two growing seasons, healthy stems and leaves near the tops of soybean were sampled for endophytic fungi. The survey yielded 1,791 isolates belonging to 17 putative species, identified by morphology and sequence analysis of the ribosomal DNA internal transcribed spacer region. Taxa were grouped by genus into operational taxonomic units: Alternaria, Colletotrichum, and Diaporthe were the dominant genera isolated. Plant parts were analyzed separately using a multivariate community analysis of isolate counts per plant. The 14.3% fluxapyroxad and 28.6% pyraclostrobin fungicide spray significantly increased the proportion of Diaporthe isolates over no-spray controls, whereas the inverse occurred for foliar Alternaria isolates. In addition, seed harvested from fields with shorter-season varieties and sprayed with fungicide showed higher percentages of Diaporthe isolates than fields with no fungicide spray. In conclusion, soybean farmers may want to consider that the application of a QoI fungicide in the absence of disease pressure might adversely impact seed quality.