scholarly journals Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens

2016 ◽  
Vol 90 (15) ◽  
pp. 6846-6863 ◽  
Author(s):  
Shin-Yi Lee Marzano ◽  
Berlin D. Nelson ◽  
Olutoyosi Ajayi-Oyetunde ◽  
Carl A. Bradley ◽  
Teresa J. Hughes ◽  
...  
Keyword(s):  
High Throughput ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Pathogenic Fungi ◽  
Plant Diseases ◽  
Plant Pathogenic Fungi ◽  
Content Type ◽  
Fungal Plant Pathogens ◽  
Viral Sequences

ABSTRACTMycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi,Colletotrichum truncatum,Macrophomina phaseolina,Diaporthe longicolla,Rhizoctonia solani, andSclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembledde novo, and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages:Barnaviridae,Benyviridae,Chrysoviridae,Endornaviridae,Fusariviridae,Hypoviridae,Mononegavirales,Narnaviridae,Ophioviridae,Ourmiavirus,Partitiviridae,Tombusviridae,Totiviridae,Tymoviridae, andVirgaviridae. More than half of the viral sequences were predicted to be members of theMitovirusgenus in the familyNarnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae,Ophioviridae, andVirgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts.IMPORTANCEPlant-pathogenic fungi reduce crop yields, which affects food security worldwide. Plant host resistance is considered a sustainable disease management option but may often be incomplete or lacking for some crops to certain fungal pathogens or strains. In addition, the rising issues of fungicide resistance demand alternative strategies to reduce the negative impacts of fungal pathogens. Those fungus-infecting viruses (mycoviruses) that attenuate fungal virulence may be welcome additions for mitigation of plant diseases. By high-throughput sequencing of the RNAs from 275 isolates of five fungal plant pathogens, 66 previously undescribed mycoviruses were identified. In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution.

scholarly journals Assessing Performance of Spore Samplers in Monitoring Aeromycobiota and Fungal Plant Pathogen Diversity in Canada

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Wen Chen ◽  
Sarah Hambleton ◽  
Keith A. Seifert ◽  
Odile Carisse ◽  
Moussa S. Diarra ◽  
...  
Keyword(s):  
Prince Edward Island ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Climatic Factors ◽  
Weather Conditions ◽  
Pilot Project ◽  
Sampling Location ◽  
Fungal Community Composition ◽  
Content Type

ABSTRACTSpore samplers are widely used in pathogen surveillance but not so much for monitoring the composition of aeromycobiota. In Canada, a nationwide spore-sampling network (AeroNet) was established as a pilot project to assess fungal community composition in air and rain samples collected using three different spore samplers in the summers of 2010 and 2011. Metabarcodes of the internal transcribed spacer (ITS) were exhaustively characterized for three of the network sites, in British Columbia (BC), Québec (QC), and Prince Edward Island (PEI), to compare performance of the samplers. Sampler type accounted for ca. 20% of the total explainable variance in aeromycobiota compositional heterogeneity, with air samplers recovering more Ascomycota and rain samplers recovering more Basidiomycota. Spore samplers showed different abilities to collect 27 fungal genera that are plant pathogens. For instance,Cladosporiumspp.,Drechsleraspp., andEntylomaspp. were collected mainly by air samplers, whileFusariumspp.,Microdochiumspp., andUstilagospp. were recovered more frequently with rain samplers. The diversity and abundance of some fungi were significantly affected by sampling location and time (e.g.,AlternariaandBipolaris) and weather conditions (e.g.,MycocentrosporaandLeptosphaeria), and depended on using ITS1 or ITS2 as the barcoding region (e.g.,EpicoccumandBotrytis). The observation that Canada's aeromycobiota diversity correlates with cooler, wetter conditions and northward wind requires support from more long-term data sets. Our vision of the AeroNet network, combined with high-throughput sequencing (HTS) and well-designed sampling strategies, may contribute significantly to a national biovigilance network for protecting plants of agricultural and economic importance in Canada.IMPORTANCEThe current study compared the performance of spore samplers for collecting broad-spectrum air- and rain-borne fungal pathogens using a metabarcoding approach. The results provided a thorough characterization of the aeromycobiota in the coastal regions of Canada in relation to the influence of climatic factors. This study lays the methodological basis to eventually develop knowledge-based guidance on pest surveillance by assisting in the selection of appropriate spore samplers.

scholarly journals Fungal Pathogens Affecting the Production and Quality of Medical Cannabis in Israel

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 882
Author(s):  
Shachar Jerushalmi ◽  
Marcel Maymon ◽  
Aviv Dombrovsky ◽  
Stanley Freeman
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Plant Diseases ◽  
Soilborne Pathogens ◽  
Medical Cannabis ◽  
Plant Parts ◽  
Commercial Cultivation

The use of and research on medical cannabis (MC) is becoming more common, yet there are still many challenges regarding plant diseases of this crop. For example, there is a lack of formal and professional knowledge regarding fungi that infect MC plants, and practical and effective methods for managing the casual agents of disease are limited. The purpose of this study was to identify foliar, stem, and soilborne pathogens affecting MC under commercial cultivation in Israel. The predominant major foliage pathogens were identified as Alternaria alternata and Botrytis cinerea, while the common stem and soilborne pathogens were identified as Fusarium oxysporum and F. solani. Other important fungi that were isolated from foliage were those producing various mycotoxins that can directly harm patients, such as Aspergillus spp. and Penicillium spp. The sampling and characterization of potential pathogenic fungi were conducted from infected MC plant parts that exhibited various disease symptoms. Koch postulates were conducted by inoculating healthy MC tissues and intact plants with fungi isolated from infected commercially cultivated symptomatic plants. In this study, we report on the major and most common plant pathogens of MC found in Israel, and determine the seasonal outbreak of each fungus.

scholarly journals Transfection of Sclerotinia sclerotiorum withIn VitroTranscripts of a Naturally Occurring Interspecific Recombinant of Sclerotinia sclerotiorum Hypovirus 2 Significantly Reduces Virulence of the Fungus

2015 ◽  
Vol 89 (9) ◽  
pp. 5060-5071 ◽  
Author(s):  
Shin-Yi Lee Marzano ◽  
Houston A. Hobbs ◽  
Berlin D. Nelson ◽  
Glen L. Hartman ◽  
Darin M. Eastburn ◽  
...  
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Infectious Clone ◽  
White Mold ◽  
Content Type ◽  
Fungal Plant Pathogens ◽  
Rapid Amplification ◽  
Valsa Ceratosperma

ABSTRACTA recombinant strain ofSclerotinia sclerotiorumhypovirus 2 (SsHV2) was identified from a North AmericanSclerotinia sclerotiorumisolate (328) from lettuce (Lactuca sativaL.) by high-throughput sequencing of total RNA. The 5′- and 3′-terminal regions of the genome were determined by rapid amplification of cDNA ends. The assembled nucleotide sequence was up to 92% identical to two recently reported SsHV2 strains but contained a deletion near its 5′ terminus of more than 1.2 kb relative to the other SsHV2 strains and an insertion of 524 nucleotides (nt) that was distantly related toValsa ceratospermahypovirus 1. This suggests that the new isolate is a heterologous recombinant of SsHV2 with a yet-uncharacterized hypovirus. We named the new strainSclerotinia sclerotiorumhypovirus 2 Lactuca (SsHV2L) and deposited the sequence in GenBank with accession numberKF898354.Sclerotinia sclerotiorumisolate 328 was coinfected with a strain ofSclerotinia sclerotiorumendornavirus 1 and was debilitated compared to cultures of the same isolate that had been cured of virus infection by cycloheximide treatment and hyphal tipping. To determine whether SsHV2L alone could induce hypovirulence inS. sclerotiorum, a full-length cDNA of the 14,538-nt viral genome was cloned. Transcripts corresponding to the viral RNA were synthesizedin vitroand transfected into a virus-free isolate ofS. sclerotiorum, DK3. Isolate DK3 transfected with SsHV2L was hypovirulent on soybean and lettuce and exhibited delayed maturation of sclerotia relative to virus-free DK3, completing Koch's postulates for the association of hypovirulence with SsHV2L.IMPORTANCEA cosmopolitan fungus,Sclerotinia sclerotioruminfects more than 400 plant species and causes a plant disease known as white mold that produces significant yield losses in major crops annually. Mycoviruses have been used successfully to reduce losses caused by fungal plant pathogens, but definitive relationships between hypovirus infections and hypovirulence inS. sclerotiorumwere lacking. By establishing a cause-and-effect relationship betweenSclerotinia sclerotiorumhypovirus Lactuca (SsHV2L) infection and the reduction in host virulence, we showed direct evidence that hypoviruses have the potential to reduce the severity of white mold disease. In addition to intraspecific recombination, this study showed that recent interspecific recombination is an important factor shaping viral genomes. The construction of an infectious clone of SsHV2L allows future exploration of the interactions between SsHV2L andS. sclerotiorum, a widespread fungal pathogen of plants.

scholarly journals Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics

mSystems ◽  
2021 ◽  
Author(s):  
Vittorio Tracanna ◽  
Adam Ossowicki ◽  
Marloes L. C. Petrus ◽  
Sam Overduin ◽  
Barbara R. Terlouw ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Amplicon Sequencing ◽  
Plant Pathogenic Fungi ◽  
Content Type ◽  
Major Threat ◽  
Wide Range

Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops.

scholarly journals Inhibition of Fungal Plant Pathogens by Aqueous Extracts of Arum cyreniacum

2021 ◽  
pp. 1-6
Author(s):  
Ahmed A. Abdulrraziq ◽  
Sami M. Salih ◽  
Sultan F. Alnomasy ◽  
Ziyad M. Aldosari ◽  
Bader S. Alotaibi
Keyword(s):  
Aspergillus Niger ◽  
Fusarium Solani ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Inhibitory Effect ◽  
Plant Pathogenic Fungi ◽  
Dependent Manner ◽  
Aqueous Extracts ◽  
Fungal Plant Pathogens ◽  
The Family

Arum cyreniacum is an important member of the family of Araceae because of its bio-activities. Hence this work aimed to establish a link between Arum cyreniacum and its uses as bio-control against plant pathogenic fungi which had never hitherto been established. This work was carried out to evaluate the activity of the aqueous extracts of tubers, leaves, and flowers of Arum cyreniacum against three different types of pathogenic fungi, Fusarium solani, Rhizopus microspores and Aspergillus niger. The antifungal activity of the aqueous extracts of Arum cyreniacum was determined by poisoned food technique. The results showed that Arum cyreniacum had an inhibitory effect in a dose-dependent manner on Fusarium solani, Rhizopus microspores, while Aspergillus niger was resistant to all extracts. However, the great inhibition activity against tested fungi was associated with increasing concentrations of the aqueous extracts of Arum cyreniacum. Data in this work indicated that the use of Arum cyreniacum could be a valid alternative for bio-control of plant pathogenic fungi.

Biodiversity of pathogenic wood fungi isolated from Xylotrechus arvicola (Olivier) galleries in vine shoots

OENO One ◽  
2013 ◽  
Vol 47 (2) ◽  
pp. 73 ◽  
Author(s):  
Pablo García Benavides ◽  
Pedro Martin Zamorano ◽  
Carlos Alvar Ocete ◽  
Lara Maistrello ◽  
Rafael Ocete
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Fungal Species ◽  
Its2 Sequence ◽  
Plant Diseases ◽  
Northern Spain ◽  
Grapevine Decline ◽  
La Rioja

<p style="text-align: justify;"><strong>Aim</strong>: Grapevine decline caused by wood fungi seriously threatens viticulture worldwide. In Spain, the polyphagous borer <em>Xylotrechus</em> <em>arvicola</em> (Coleoptera, Cerambycidae) is becoming a serious pest in different Qualified Designation of Origin (DOC) wine regions. The aim of the present work was to identify the fungal species growing in the galleries excavated by <em>X. arvicola</em> larvae inside the vine branches and investigate the possible relationship between wood pathogenic fungi and this borer.</p><p style="text-align: justify;"><strong>Methods and results</strong>: Wood samples from branches of Tempranillo vines and <em>Prunus pisardi</em> trees affected by the borer <em>X. arvicola</em> were collected in La Rioja DOC vineyards (Northern Spain) and analyzed for the presence of fungi using both morphological techniques and genetic tools based on Internal Transcribed Spacer 2 (ITS2) sequence. Among the 20 different fungal species/isolates identified, 7 belonged to fungi associated with grapevine decline (esca, Petri disease, and <em>Eutypa</em> dieback), 6 were plant pathogens, 6 were saprophytic and one was entomopathogenic (<em>Beauveria bassiana</em>).</p><p style="text-align: justify;"><strong>Conclusion</strong>: The fact that 65 % of the fungi detected inside <em>X. arvicola</em> galleries belong to species recognized as plant pathogens suggests that this borer, in addition to causing a progressive decay of the branches, could facilitate the transmission of plant diseases, further threatening the vineyards by spreading grapevine decline pathogens.</p><p style="text-align: justify;"><strong>Significance and impact of the study</strong>: The present work represents a first step in recognizing the association between the fungal pathogens associated with grapevine decline and the borer <em>X. arvicola</em>, suggesting a possible role of this insect as a vector in the transmission of these fungi.</p>

scholarly journals Genus-Specific Primers for Study of Fusarium Communities in Field Samples

2015 ◽  
Vol 82 (2) ◽  
pp. 491-501 ◽  
Author(s):  
Ida Karlsson ◽  
Véronique Edel-Hermann ◽  
Nadine Gautheron ◽  
Mikael Brandström Durling ◽  
Anna-Karin Kolseth ◽  
...  
Keyword(s):  
High Throughput ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Elongation Factor ◽  
Specific Primers ◽  
Translation Elongation ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Field Samples ◽  
High Discriminatory Power

ABSTRACTFusariumis a large and diverse genus of fungi of great agricultural and economic importance, containing many plant pathogens and mycotoxin producers. To date, high-throughput sequencing ofFusariumcommunities has been limited by the lack of genus-specific primers targeting regions with high discriminatory power at the species level. In the present study, we evaluated twoFusarium-specific primer pairs targeting translation elongation factor 1 (TEF1). We also present the new primer pair Fa+7/Ra+6. MockFusariumcommunities reflecting phylogenetic diversity were used to evaluate the accuracy of the primers in reflecting the relative abundance of the species. TEF1 amplicons were subjected to 454 high-throughput sequencing to characterizeFusariumcommunities. Field samples from soil and wheat kernels were included to test the method on more-complex material. For kernel samples, a single PCR was sufficient, while for soil samples, nested PCR was necessary. The newly developed primer pairs Fa+7/Ra+6 and Fa/Ra accurately reflectedFusariumspecies composition in mock DNA communities. In field samples, 47Fusariumoperational taxonomic units were identified, with the highestFusariumdiversity in soil. TheFusariumcommunity in soil was dominated by members of theFusarium incarnatum-Fusarium equisetispecies complex, contradicting findings in previous studies. The method was successfully applied to analyzeFusariumcommunities in soil and plant material and can facilitate further studies ofFusariumecology.

scholarly journals One cut to change them all: CRISPR/Cas, a groundbreaking tool for genome editing in Botrytis cinerea and other fungal plant pathogens

2020 ◽  
Author(s):  
Matthias Hahn ◽  
Gabriel Scalliet
Keyword(s):  
Genome Editing ◽  
Botrytis Cinerea ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Plant Pathogenic Fungi ◽  
Antifungal Compounds ◽  
Fungal Plant Pathogens ◽  
A Genome ◽  
Functional Biology ◽  
Cas A

CRISPR/Cas is a genome editing technology that has opened new dimensions in functional biology. In a recent publication, we present a highly efficient CRISPR/Cas technique for Botrytis cinerea, which dramatically increases our options to mutagenize and modify single or multiple genes. In this Perspectives article, we describe the essential features of the method, and demonstrate with several examples how it opens new avenues for unravelling the virulence mechanisms of Botrytis and other plant pathogenic fungi, and to accelerate research for the identification of new antifungal compounds.

scholarly journals Importance of Molecular Data to Identify Fungal Plant Pathogens and Guidelines for Pathogenicity Testing Based on Koch’s Postulates

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1096
Author(s):  
Chitrabhanu S. Bhunjun ◽  
Alan J. L. Phillips ◽  
Ruvishika S. Jayawardena ◽  
Itthayakorn Promputtha ◽  
Kevin D. Hyde
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Molecular Data ◽  
Plant Diseases ◽  
Koch’S Postulates ◽  
Disease Symptoms ◽  
Fungal Plant Pathogens ◽  
Bradford Hill ◽  
Pathogenicity Testing ◽  
Koch's Postulates

Fungi are an essential component of any ecosystem, but they can also cause mild and severe plant diseases. Plant diseases are caused by a wide array of fungal groups that affect a diverse range of hosts with different tissue specificities. Fungi were previously named based only on morphology and, in many cases, host association, which has led to superfluous species names and synonyms. Morphology-based identification represents an important method for genus level identification and molecular data are important to accurately identify species. Accurate identification of fungal pathogens is vital as the scientific name links the knowledge concerning a species including the biology, host range, distribution, and potential risk of the pathogen, which are vital for effective control measures. Thus, in the modern era, a polyphasic approach is recommended when identifying fungal pathogens. It is also important to determine if the organism is capable of causing host damage, which usually relies on the application of Koch’s postulates for fungal plant pathogens. The importance and the challenges of applying Koch’s postulates are discussed. Bradford Hill criteria, which are generally used in establishing the cause of human disease, are briefly introduced. We provide guidelines for pathogenicity testing based on the implementation of modified Koch’s postulates incorporating biological gradient, consistency, and plausibility criteria from Bradford Hill. We provide a set of protocols for fungal pathogenicity testing along with a severity score guide, which takes into consideration the depth of lesions. The application of a standard protocol for fungal pathogenicity testing and disease assessment in plants will enable inter-studies comparison, thus improving accuracy. When introducing novel plant pathogenic fungal species without proving the taxon is the causal agent using Koch’s postulates, we advise the use of the term associated with the “disease symptoms” of “the host plant”. Where possible, details of disease symptoms should be clearly articulated.

scholarly journals Isolation and Characterization of Trichoderma Strains Antagonistic Against Pathogenic Fungi on Orange Crops

2020 ◽  
Vol 36 (3) ◽  
Author(s):  
Vu Xuan Tao ◽  
Tran Van Tuan
Keyword(s):  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Morphological Characteristics ◽  
Its Region ◽  
Pathogenic Fungi ◽  
Phytophthora Species ◽  
Fruit Rot ◽  
Trichoderma Species ◽  
Isolation And Characterization ◽  
Fungal Plant Pathogens

Agricultural production is greatly influenced by diseases caused by fungi. Penicillium digitatum is a common fungus that causes blue mold in citrus fruits. In addition, Fusarium and Phytophthora species are also recognized as citrus pathogens, involving in root rot and fruit rot. Currently, the use of microbial bioproducts to control fungal pathogens is always prioritized for an organic and sustainable agriculture. Trichoderma species are considered as safe filamentous fungi that antagonize against many fungal plant pathogens. In this study, 10 strains of Trichoderma were isolated and monitored for their antagonistic capacity towards the citrus pathogen P. digitatum. The strains Trichoderma Tr.6, Tr.7 and Tr.8 exhibited inhibitory efficacy of 95-100% against P. digitatum. Additionally, these three strains also strongly suppressed the growth of two other common plant pathogens Fusarium oxysporum and Phytophthora capsici. Based on the morphological characteristics and the sequence analysis of the internal transcribed spacer (ITS) region of rDNA, all three strains Tr.6, Tr.7 and Tr.8 were identified as Trichoderma asperellum. These Trichoderma strains represent promising potentials for applications in the production of bioproducts for the control of pathogenic fungi infecting citrus and other crops.

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