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 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 Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

Cyclic hexadepsipeptides in wheat field samples and esyn1 gene divergence among enniatin producing Fusarium avenaceum strains

2013 ◽  
Vol 6 (4) ◽  
pp. 399-409 ◽  
Author(s):  
Ł. Stȩpień ◽  
M. Jestoi ◽  
J. Chełkowski
Keyword(s):  
Elongation Factor ◽  
Fusarium Avenaceum ◽  
Translation Elongation ◽  
Wheat Field ◽  
Separate Branch ◽  
Field Samples ◽  
Species Specific ◽  
Wheat Kernels ◽  
Moderate Climate ◽  
Translation Elongation Factor 1Α

Fusarium avenaceum is one of the most important pathogenic species in agricultural and forest environments of moderate climate, particularly in cereals and legume pulse crops. Numerous mycotoxins can be synthesized by the species, with moniliformin and enniatins (ENN) being the prevailing metabolites. The aims of this work were to examine the amounts of ENN and beauvericin present in naturally contaminated field samples of wheat kernels and chaffs collected in Poland in 2005 and 2009 from heads infected with F. avenaceum, and to reveal the divergence of the esyn1 gene among F. avenaceum strains of different origin. ENN-B and ENN-B1 were the major metabolites identified in wheat field samples. Chaff fractions contained significantly more mycotoxins than grain. Samples originating from 2005 were in general less contaminated with ENN than those from the 2009 season. The highest amount of ENN-B found in grain was 28,520 μg/kg. Beauvericin was only found in trace amounts in all the samples tested. F. avenaceum strains isolated from the analysed wheat samples were identified using species-specific DNA marker and translation elongation factor 1α (tef-1α) sequence analysis. A higher level of sequence polymorphism was revealed for the enniatin synthetase (esyn1) gene than ecorded by tef-1α analysis. Moreover, species known to be typical beauvericin producers, e.g. Fusarium oxysporum and Fusarium proliferatum, were clustered into a separate branch on the dendrogram, apart from the strains of ENN-producing species, i.e. F. avenaceum and Fusarium scirpi.

scholarly journals Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

MycoKeys ◽  
2018 ◽  
Vol 39 ◽  
pp. 29-40 ◽  
Author(s):  
Sten Anslan ◽  
R. Henrik Nilsson ◽  
Christian Wurzbacher ◽  
Petr Baldrian ◽  
Leho Tedersoo ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Computation Time ◽  
Potential Effect ◽  
Data Sets ◽  
Sequencing Data ◽  
Operational Taxonomic Units ◽  
High Throughput Sequencing Data ◽  
Recent Developments

Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

scholarly journals Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

2017 ◽  
Vol 83 (22) ◽  
Author(s):  
Konstantia Gkarmiri ◽  
Shahid Mahmood ◽  
Alf Ekblad ◽  
Sadhna Alström ◽  
Nils Högberg ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Stable Isotope ◽  
Oilseed Rape ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Stable Isotope Probing ◽  
Biofuel Production ◽  
Content Type ◽  
Bacteria And Fungi

ABSTRACT RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. “Candidatus Nitrososphaera” was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus. IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

scholarly journals Identification and Characterization of Diaporthe ambigua, D. australafricana, D. novem, and D. rudis Causing a Postharvest Fruit Rot in Kiwifruit

Plant Disease ◽  
2017 ◽  
Vol 101 (8) ◽  
pp. 1402-1410 ◽  
Author(s):  
Gonzalo A. Díaz ◽  
Bernardo A. Latorre ◽  
Mauricio Lolas ◽  
Enrique Ferrada ◽  
Paulina Naranjo ◽  
...  
Keyword(s):  
San Francisco ◽  
Plant Pathogens ◽  
Elongation Factor ◽  
Its Region ◽  
Fruit Rot ◽  
Lesion Length ◽  
Translation Elongation ◽  
Wide Range ◽  
Postharvest Rot ◽  
Diaporthe Ambigua

Diaporthe spp. are important plant pathogens causing wood cankers, blight, dieback, and fruit rot in a wide range of hosts. During surveys conducted during the 2013 and 2014 seasons, a postharvest rot in Hayward kiwifruit (Actinidia deliciosa) was observed in Chile. In order to identify the species of Diaporthe associated with this fruit rot, symptomatic fruit were collected from seven kiwifruit packinghouses located between San Francisco de Mostazal and Curicó (central Chile). Twenty-four isolates of Diaporthe spp. were identified from infected fruit based on morphological and cultural characters and analyses of nucleotides sequences of three loci, including the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2), a partial sequences of the β-tubulin, and translation elongation factor 1-α genes. The Diaporthe spp. identified were Diaporthe ambigua, D. australafricana, D. novem, and D. rudis. Multilocus phylogenetic analysis revealed that Chilean isolates were grouped in separate clades with their correspondent ex-types species. All species of Diaporthe were pathogenic on wounded kiwifruit after 30 days at 0°C under normal and controlled-atmosphere (2% O2 and 5% CO2) storage and they were sensitive to benomyl, pyraclostrobin, and tebuconazole fungicides. D. ambigua isolates were the most virulent based on the lesion length measured in inoculated Hayward and Jintao kiwifruit. These findings confirm D. ambigua, D. australafricana, D. novem, and D. rudis as the causal agents of kiwifruit rot during cold storage in Chile. The specie D. actinidiae, a common of Diaporthe sp. found associated with kiwifruit rot, was not identified in the present study.

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.

Identification of Pathogenic Fusarium spp. Responsible for Root Rot of Angelica sinensis and Characterization of their Biological Enemies in Dingxi, China

Plant Disease ◽  
2022 ◽  
Author(s):  
Liu Yang ◽  
Tian Yuan ◽  
Xia Zhao ◽  
Yue Liang ◽  
UWAREMWE CONSTANTINE ◽  
...  
Keyword(s):  
Root Rot ◽  
Elongation Factor ◽  
Its Region ◽  
Fungal Species ◽  
Cortical Cells ◽  
Translation Elongation ◽  
Field Samples ◽  
Fusarium Pathogens ◽  
Rot Disease ◽  
Serious Disease

Root rot is a serious disease in plantations of A. sinensis, severely affecting yield and quality and threatening sustainable production. Fusarium isolates (n=32) were obtained from field samples of root rot tissue, leaves and infected soil. Isolates were identified by comparing the sequences of their internal transcribed spacer (ITS) region and translation elongation factor 1-ɑ (TEF-1ɑ) to sequences of known species in the NCBI-database. These Fusarium isolates include F. tricinctum (43.75%), F. equiseti (31.25%), F. solani (9.37%), F. oxysporum (6.25%), F. acuminatum (6.25%), and F. incarnatum (3.12%). For pathogenicity testing under greenhouse conditions, seven isolates were selected based on a phylogenetic analysis, including four strains of F. tricinctum and one strain each of F. solani, F. oxysporum, and F. acuminatum. The seven isolates were all pathogenic but differed in their ability to infect: the four F. tricinctum strains were capable pathogens causing root rot in A. sinensis at 100% incidence and the highly aggressive. Furthermore, the symptoms of root rot induced by those seven isolates were consistent with typical root rot cases in the field, but their disease severity varied. Observed histopathological preparations of F. tricinctum-infected seedlings and tissue-slides results showed this fungal species can penetrate epidermal cells and colonize the cortical cells where it induces necrosis and severe plasmolysis. Plate confrontation experiments showed that isolated rhizosphere bacteria inhibited the Fusarium pathogens that cause root rot in A. sinensis. Our results provide timely information for informing the use of biocontrol agents for suppression of root rot disease.

Effect of Plantaricin 163 in Combination with Thymol and Surfactin on Crucian Carp (Carassius auratus)

2019 ◽  
Vol 82 (8) ◽  
pp. 1283-1291 ◽  
Author(s):  
HECHAO DU ◽  
XIUXIU LI ◽  
ZHAOXIN LU ◽  
XIAOMEI BIE ◽  
HAIZHEN ZHAO ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Crucian Carp ◽  
Thiobarbituric Acid ◽  
Commercial Application ◽  
Operational Taxonomic Units ◽  
Spoilage Bacteria ◽  
Plate Counts ◽  
Natural Preservatives ◽  
Control Samples

ABSTRACT The use of natural preservatives has attracted considerable attention owing to their generally safe and environmentally friendly properties. In this study, we investigated the effects of the preservative A1, composed of plantaricin 163, thymol, and surfactin, on bacterial communities and storage quality of refrigerated crucian carp. A total of 522 operational taxonomic units belonging to 20 phyla and 272 genera were identified by high-throughput sequencing, showing a comprehensive coverage of bacterial composition of crucian carp. In untreated samples after spoilage, Brochothrix was the predominant genus, followed by Aeromonas and Pseudomonas. After treatment with A1, the growth of these spoilage bacteria was significantly inhibited according to high-throughput sequencing and plate counts, and Lactococcus became the most abundant organism at the end of storage. Meanwhile, compared with control samples, the shelf life of A1-treated samples extended from 3 to 12 days on the basis of the sensory evaluation and the total viable counts. Furthermore, the total volatile basic nitrogen, thiobarbituric acid, and pH values for A1-treated samples were significantly lower than that of control samples. The results indicate that preservative A1 has potential commercial application in the preservation of refrigerated crucian carp.

Sign in / Sign up

Export Citation Format

Share Document