scholarly journals RNA-Based Analysis Reveals High Diversity of Plant-Associated Active Fungi in the Atmosphere

2021 ◽  
Vol 12 ◽  
Author(s):  
Yan Chen ◽  
Xishen Zhu ◽  
Ziqiong Hou ◽  
Yi Wang ◽  
Yunying Zhou ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Essential Feature ◽  
Pathogenic Fungi ◽  
Amplicon Sequencing ◽  
Airborne Fungi ◽  
Sequencing Analysis ◽  
Human Pathogens ◽  
Long Distance ◽  
Airborne Microbes ◽  
New Perspective

Fungi are ubiquitous in nature; that is, they are present everywhere on the planet; understanding the active state and functional capacity of airborne microbes associated with health of human, animal, and plant is critical for biosafety management. Here, we firstly and directly proved that there were about 40% active fungi in the air via rRNA amplicon sequencing and imaging flow cytometry simultaneously. Amplicon sequencing analysis showed differences between structures of active and total fungal community; Ascomycota were dominant in the active community, while Basidiomycota have low transcriptional activity across all samples. Notably, plant pathogenic fungi were predominant in the air, and more than 50% were active, including not only several common plant pathogens but also biotrophic fungi (Erysiphe sp. and Microbotryum sp.) and host-specific pathogens, which were generally considered to be inactive after leaving the host. Putative plant pathogens of eight genera were found active across the sampling season, indicating their superior ability to obtain nutrients even in barren nutrient environments. Interestingly, we detected several potentially active unrecorded fungi in China (Diatrype prominens, Septofusidium herbarum, Pseudomicrostroma glucosiphilum, and Uromycladium tepperianum), which suggested that they spread over a long distance by air and may cause diseases under favorable conditions. Our results suggested that maintaining transmission in air is an essential feature of many fungi including plant pathogens regardless of being a biotrophic, hemibiotrophic, or necrotrophic group. Moreover, two potentially active human pathogens and one animal pathogen were captured, which indicated their potential risks. This study provided a new perspective for more comprehensive understanding of airborne fungi, including their multidimensional lifestyle, state, functioning, and potential pathogenic risk. It also laid the foundation for further prediction and management of airborne microbial communities, which would be of interest for public health and agriculture.

scholarly journals Isolation and Identification of Antibiotic-Producing Halophilic Bacteria from Dagh Biarjmand and Haj Aligholi Salt Deserts, Iran

2019 ◽  
Vol 25 (1) ◽  
pp. 70-77 ◽  
Author(s):  
Babak Elyasifar ◽  
Sevda Jafari ◽  
Somayeh Hallaj-Nezhadi ◽  
Florence Chapeland-leclerc ◽  
Gwenaël Ruprich-Robert ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Plant Pathogens ◽  
Halophilic Bacteria ◽  
Pathogenic Fungi ◽  
Antibacterial Activities ◽  
Biochemical Properties ◽  
Diffusion Method ◽  
Human Pathogens ◽  
Isolation And Identification ◽  
Phylogenic Tree

Background: Halophilic bacteria are potent organisms in production of novel bioactive antimicrobial compounds which might be considered in drug innovation and control of plant pathogens. Salt deserts in Semnan province are of the most permanent hypersaline areas in the North of Iran. Despite the importance of these areas, there is no scientific report regarding the biodiversity and potency of their halophilic bacteria. Thus, aforementioned areas were selected to detect the halophilic bacteria. Methods: Here, seven strains were isolated and cultured on their molecular and biochemical properties were characterized. To determine the antibiotic potency of the isolates, agar well diffusion method was conducted. Phylogenetic analysis was done to reveal the isolates relationship with previously known strains. Results: As a result, growth of the strains in the medium containing 5 to 20% (w/v) NaCl determined that the majority of the isolates were moderately halophile. Catalase activity of all strains was positive. The results represented that D6A, Dar and D8B have antimicrobial effects against different plant and human pathogens. Phylogenic tree analysis also showed that two strains of D6A and Dar are belonged to Bacillus subtilis and D8B is belonged to Virgibacillus olivae. The bacteria extracts were evaluated for their antifungal and antibacterial activities on human and Plant pathogenic strains. The MIC of the extract B. subtilis against was found active against human pathogenic fungi and Plant pathogenic bacteria and fungi, ranging from 12.5 to 25 µg/mL. Conclusion: This study highlights the therapeutic and prophylactic potential of B. subtilis extracts as antibacterial and antifungal agents.

scholarly journals Pathogenic potential prediction for novel fungal DNA based on a curated fungi-hosts data collection

2021 ◽  
Author(s):  
Jakub M Bartoszewicz ◽  
Ferdous Nasri ◽  
Melania Nowicka ◽  
Bernhard Y Renard
Keyword(s):  
Data Collection ◽  
Dna Sequences ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Range Data ◽  
Human Pathogens ◽  
Sequencing Data ◽  
Emerging Pathogens ◽  
Pathogenic Potential ◽  
Fungal Host

Background: Emerging pathogens are a growing threat, but large data collections and approaches for predicting the risk associated with novel agents are limited to bacteria and viruses. Pathogenic fungi, which also pose a constant threat to public health, remain understudied. Relevant, curated data remains comparatively scarce and scattered among many different sources, hindering the development of sequencing-based detection workflows for novel fungal pathogens. No prediction method working for agents across all three groups is available, even though the cause of an infection is often difficult to identify from symptoms alone. Results: We present a curated collection of fungal host range data, comprising records on human, animal and plant pathogens, as well as other plant-associated fungi, linked to publicly available genomes. We show that the resulting database can be used to predict the pathogenic potential of novel fungal species directly from DNA sequences with either sequence homology or deep learning. We develop learned, numerical representations of the collected genomes and show that the human pathogens are separable from non-human pathogens. Finally, we train multi-class models predicting if next-generation sequencing reads originate from novel fungal, bacterial or viral threats. Conclusions: The presented data collection enables accurate detection of novel pathogens from sequencing data. It is also a comprehensive resource that can find use beyond this particular task. This can include possible applications in proteomics and genomics, employing both machine learning and direct sequence comparison. Availability: The database and models are hosted at https://zenodo.org/record/5711852 and https://zenodo.org/record/5711877. Source code is available at https://gitlab.com/dacs-hpi/deepac.

Deep-Amplicon Sequencing(DAS) to evidence the presesence of human pathogens in drinking water

2020 ◽  
Author(s):  
Laura Moreno-Mesonero ◽  
Jorge García Hernández ◽  
Yolanda Moreno ◽  
PATRICIA SOLER
Keyword(s):  
Drinking Water ◽  
Amplicon Sequencing ◽  
Human Pathogens

scholarly journals The impact of bZIP Atf1ortholog global regulators in fungi

2021 ◽  
Author(s):  
Éva Leiter ◽  
Tamás Emri ◽  
Klaudia Pákozdi ◽  
László Hornok ◽  
István Pócsi
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Secondary Metabolite ◽  
Plant Pathogens ◽  
Leucine Zipper ◽  
Secondary Metabolite Production ◽  
Special Focus ◽  
Human Pathogens ◽  
Metabolite Production ◽  
The Impact

Abstract Regulation of signal transduction pathways is crucial for the maintenance of cellular homeostasis and organismal development in fungi. Transcription factors are key elements of this regulatory network. The basic-region leucine zipper (bZIP) domain of the bZIP-type transcription factors is responsible for DNA binding while their leucine zipper structural motifs are suitable for dimerization with each other facilitiating the formation of homodimeric or heterodimeric bZIP proteins. This review highlights recent knowledge on the function of fungal orthologs of the Schizosaccharomyces pombe Atf1, Aspergillus nidulans AtfA, and Fusarium verticillioides FvAtfA, bZIP-type transcription factors with a special focus on pathogenic species. We demonstrate that fungal Atf1-AtfA-FvAtfA orthologs play an important role in vegetative growth, sexual and asexual development, stress response, secondary metabolite production, and virulence both in human pathogens, including Aspergillus fumigatus, Mucor circinelloides, Penicillium marneffei, and Cryptococcus neoformans and plant pathogens, like Fusarium ssp., Magnaporthe oryzae, Claviceps purpurea, Botrytis cinerea, and Verticillium dahliae. Key points • Atf1 orthologs play crucial role in the growth and development of fungi. • Atf1 orthologs orchestrate environmental stress response of fungi. • Secondary metabolite production and virulence are coordinated by Atf1 orthologs.

scholarly journals The Ustilago hordei–Barley Interaction is a Versatile System for Characterization of Fungal Effectors

2021 ◽  
Vol 7 (2) ◽  
pp. 86
Author(s):  
Bilal Ökmen ◽  
Daniela Schwammbach ◽  
Guus Bakkeren ◽  
Ulla Neumann ◽  
Gunther Doehlemann
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Expression System ◽  
Pathogenic Fungi ◽  
Effector Proteins ◽  
Mating Partner ◽  
Fungal Virulence ◽  
Functional Studies ◽  
Infection Structures ◽  
Ustilago Hordei

Obligate biotrophic fungal pathogens, such as Blumeria graminis and Puccinia graminis, are amongst the most devastating plant pathogens, causing dramatic yield losses in many economically important crops worldwide. However, a lack of reliable tools for the efficient genetic transformation has hampered studies into the molecular basis of their virulence or pathogenicity. In this study, we present the Ustilago hordei–barley pathosystem as a model to characterize effectors from different plant pathogenic fungi. We generate U. hordei solopathogenic strains, which form infectious filaments without the presence of a compatible mating partner. Solopathogenic strains are suitable for heterologous expression system for fungal virulence factors. A highly efficient Crispr/Cas9 gene editing system is made available for U. hordei. In addition, U. hordei infection structures during barley colonization are analyzed using transmission electron microscopy, showing that U. hordei forms intracellular infection structures sharing high similarity to haustoria formed by obligate rust and powdery mildew fungi. Thus, U. hordei has high potential as a fungal expression platform for functional studies of heterologous effector proteins in barley.

scholarly journals Information Length as a Useful Index to Understand Variability in the Global Circulation

Mathematics ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 299 ◽  
Author(s):  
Eun-jin Kim ◽  
James Heseltine ◽  
Hanli Liu
Keyword(s):  
Climate Model ◽  
Traditional Approach ◽  
Essential Feature ◽  
Complex Form ◽  
Time Dependent ◽  
Spatial Gradient ◽  
Mean Values ◽  
Global Circulation ◽  
New Perspective ◽  
Non Gaussian

With improved measurement and modelling technology, variability has emerged as an essential feature in non-equilibrium processes. While traditionally, mean values and variance have been heavily used, they are not appropriate in describing extreme events where a significant deviation from mean values often occurs. Furthermore, stationary Probability Density Functions (PDFs) miss crucial information about the dynamics associated with variability. It is thus critical to go beyond a traditional approach and deal with time-dependent PDFs. Here, we consider atmospheric data from the Whole Atmosphere Community Climate Model (WACCM) and calculate time-dependent PDFs and the information length from these PDFs, which is the total number of statistically different states that a system evolves through in time. Specifically, we consider the three cases of sampling data to investigate the distribution of information (information budget) along the altitude and longitude to gain a new perspective of understanding variabilities, correlation among different variables and regions. Time-dependent PDFs are shown to be non-Gaussian in general; the information length tends to increase with the altitude albeit in a complex form; this tendency is more robust for flows/shears than temperature. Much similarity among flows and shears in the information length is also found in comparison with the temperature. This means a strong correlation among flows/shears because of their coupling through gravity waves in this particular WACCM model. We also find the increase of the information length with the latitude and interesting hemispheric asymmetry for flows/shears/temperature, with the tendency of anti-correlation (correlation) between flows/shears and temperature at high (low) latitude. These results suggest the importance of high latitude/altitude in the information budget in the Earth’s atmosphere, the spatial gradient of the information length being a useful proxy for information flow.

scholarly journals Double Gamers—Can Modified Natural Regulators of Higher Plants Act as Antagonists against Phytopathogens? The Case of Jasmonic Acid Derivatives

2020 ◽  
Vol 21 (22) ◽  
pp. 8681
Author(s):  
Nicolò Orsoni ◽  
Francesca Degola ◽  
Luca Nerva ◽  
Franco Bisceglie ◽  
Giorgio Spadola ◽  
...  
Keyword(s):  
Jasmonic Acid ◽  
Plant Pathogens ◽  
Higher Plants ◽  
Fungal Growth ◽  
Pathogenic Fungi ◽  
Inhibitory Effect ◽  
Fungal Species ◽  
Phytopathogenic Fungi ◽  
Phaeomoniella Chlamydospora ◽  
Horticultural Crops

As key players in biotic stress response of plants, jasmonic acid (JA) and its derivatives cover a specific and prominent role in pathogens-mediated signaling and hence are promising candidates for a sustainable management of phytopathogenic fungi. Recently, JA directed antimicrobial effects on plant pathogens has been suggested, supporting the theory of oxylipins as double gamers in plant-pathogen interaction. Based on these premises, six derivatives (dihydrojasmone and cis-jasmone, two thiosemicarbazonic derivatives and their corresponding complexes with copper) have been evaluated against 13 fungal species affecting various economically important herbaceous and woody crops, such as cereals, grapes and horticultural crops: Phaeoacremonium minimum, Neofusicoccum parvum, Phaeomoniella chlamydospora, Fomitiporia mediterranea, Fusarium poae, F. culmorum, F. graminearum, F. oxysporum f. sp. lactucae,F. sporotrichioides, Aspergillus flavus, Rhizoctonia solani,Sclerotinia spp. and Verticillium dahliae. The biological activity of these compounds was assessed in terms of growth inhibition and, for the two mycotoxigenic species A. flavus and F. sporotrichioides, also in terms of toxin containment. As expected, the inhibitory effect of molecules greatly varied amongst both genera and species; cis-jasmone thiosemicarbazone in particular has shown the wider range of effectiveness. However, our results show that thiosemicarbazones derivatives are more effective than the parent ketones in limiting fungal growth and mycotoxins production, supporting possible applications for the control of pathogenic fungi.

Dynamics of fungal pathogens in host plant tissues

1995 ◽  
Vol 73 (S1) ◽  
pp. 1275-1283 ◽  
Author(s):  
Shigehito Takenaka
Keyword(s):  
Host Plant ◽  
Species Interactions ◽  
Fungal Biomass ◽  
Quantitative Methods ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Molecular Methods ◽  
Plant Colonization ◽  
Fungal Colonization ◽  
Plant Tissues

To develop efficient control measures against fungal plant pathogens, the dynamics of host plant colonization during disease development and the interactions among fungi within host plant tissues need to be clarified. These studies require accurate quantitative estimation of specific fungal biomass in plant tissues. This has been approached by direct-microscopic methods, cultural methods, chemical determinations of fungal components, serological methods, and molecular methods. Among these methods, serological and molecular methods provide rapid, specific, and sensitive quantitative measures of fungal biomass in host plant tissues. Therefore, studies on fungal dynamics of host plant colonization using these two methods are presented. Some examples of species interactions among pathogenic fungi within host plants, such as synergism and competition, are reviewed and the usefulness of serological and molecular methods for studies on these interactions is presented. These quantitative methods will provide helpful information for understanding the ecology of plant pathogenic fungi, such as the dynamics of host plant colonization and species interactions. Key words: quantitative methods, fungal biomass, ELISA, PCR, fungal colonization, species interaction.

scholarly journals Spray-induced gene silencing for disease control is dependent on the efficiency of pathogen RNA uptake

2021 ◽  
Author(s):  
Lulu Qiao ◽  
Chi Lan ◽  
Luca Capriotti ◽  
Audrey Ah-Fong ◽  
Jonatan Nino Sanchez ◽  
...  
Keyword(s):  
Disease Management ◽  
Plant Disease ◽  
Plant Pathogens ◽  
Developmental Stages ◽  
Pathogenic Fungi ◽  
Cell Types ◽  
Uptake Efficiency ◽  
Fungal Plant Pathogens ◽  
Plant Disease Management ◽  
Fungal Genes

AbstractRecent discoveries show that fungi can take up environmental RNA, which can then silence fungal genes through environmental RNA interference. This discovery prompted the development of Spray-Induced Gene Silencing (SIGS) for plant disease management. In this study, we aimed to determine the efficacy of SIGS across a variety of eukaryotic microbes. We first examined the efficiency of RNA uptake in multiple pathogenic and non-pathogenic fungi, and an oomycete pathogen. We observed efficient double-stranded RNA (dsRNA) uptake in the fungal plant pathogens Botrytis cinerea, Sclerotinia sclerotiorum, Rhizoctonia solani, Aspergillus niger, and Verticillium dahliae, but no uptake in Colletotrichum gloeosporioides, and weak uptake in a beneficial fungus, Trichoderma virens. For the oomycete plant pathogen, Phytophthora infestans, RNA uptake was limited, and varied across different cell types and developmental stages. Topical application of dsRNA targeting virulence-related genes in the pathogens with high RNA uptake efficiency significantly inhibited plant disease symptoms, whereas the application of dsRNA in pathogens with low RNA uptake efficiency did not suppress infection. Our results have revealed that dsRNA uptake efficiencies vary across eukaryotic microbe species and cell types. The success of SIGS for plant disease management can largely be determined by the pathogen RNA uptake efficiency.

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