scholarly journals Pythium spp. Associated with Rooibos Seedlings, and Their Pathogenicity Toward Rooibos, Lupin, and Oat

Plant Disease ◽  
2014 ◽  
Vol 98 (2) ◽  
pp. 223-232 ◽  
Author(s):  
Amirhossein Bahramisharif ◽  
Sandra C. Lamprecht ◽  
Christoffel F. J. Spies ◽  
Wilhelm J. Botha ◽  
Frikkie J. Calitz ◽  
...  
Keyword(s):  
Phytophthora Cinnamomi ◽  
Phylogenetic Analyses ◽  
Common Species ◽  
Limited Information ◽  
Internal Transcribed Spacer Region ◽  
Pythium Irregulare ◽  
Rotation Crops ◽  
Native Site ◽  
Highly Virulent ◽  
Pythium Acanthicum

Rooibos (Aspalathus linearis) is an important indigenous crop in South Africa. Oomycetes are a common problem in rooibos nurseries, causing serious losses, but limited information is available on the species involved. Molecular and morphological analyses of 117 oomycete isolates from 19 rooibos nurseries and 33 isolates from 11 native rooibos sites revealed the presence of several Pythium spp., including Pythium acanthicum, P. irregulare, P. mamillatum, P. myriotylum, P. pyrilobum, P. cederbergense, and Pythium RB II, and Phytophthora cinnamomi (native site). Most of the species were identified in nurseries and native rooibos, with Pythium irregulare being the most common species occurring in all nurseries and 46% of the native sites. Phylogenetic analyses of the internal transcribed spacer region of the P. irregulare isolates showed that isolates within this species complex fit into three subclades, of which only two have previously been reported. On rooibos, all species except P. acanthicum and the previously characterized P. cederbergense and Pythium RB II were pathogenic and highly virulent. On lupin and oat, rotation crops in nurseries, the three aforementioned species were also nonpathogenic. All the other oomycete species were pathogenic on lupin but less so than on rooibos. On oat, only P. irregulare, P. myriotylum, and P. pyrilobum were pathogenic. This is the first report of P. mamillatum, P. pyrilobum, and P. myriotylum as pathogens of lupin, and P. irregulare and P. pyrilobum as pathogens of oat. The three nonpathogenic Pythium spp. were able to significantly reduce disease caused by pathogenic species in the less susceptible lupin and oat but not on rooibos. On lupin, the nonpathogenic species enhanced the virulence of Phytophthora cinnamomi.

scholarly journals Diversity and Antimicrobial Resistance in the Streptococcus bovis/Streptococcus equinus Complex (SBSEC) Isolated from Korean Domestic Ruminants

2021 ◽  
Vol 9 (1) ◽  
pp. 98
Author(s):  
Seon Young Park ◽  
Mingyung Lee ◽  
Se Ra Lim ◽  
Hyemin Kwon ◽  
Ye Seul Lee ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Phylogenetic Analyses ◽  
Tetracycline Resistance ◽  
Current Status ◽  
Streptococcus Bovis ◽  
Limited Information ◽  
Phenotypic Resistance ◽  
Domestic Ruminants ◽  
Antimicrobial Resistance Genes ◽  
Acid Producing Bacteria

S. bovis/S. equinus complex (SBSEC) includes lactic acid-producing bacteria considered as the causative agent associated with acute rumen lactic acidosis in intensive ruminants. Considering the limited information on the detailed characteristics and diversity of SBSEC in Korea and the emergence of antimicrobial resistance (AMR), we investigated the diversity of SBSEC from domestic ruminants and verified the presence of antimicrobial resistance genes (ARGs) against several antimicrobials with their phenotypic resistance. Among 51 SBSEC isolates collected, two SBSEC members (S. equinus and S. lutetiensis) were identified; sodA-based phylogenetic analyses and comparisons of overall genome relatedness revealed potential plasticity and diversity. The AMR rates of these SBSEC against erythromycin, clindamycin, and tetracycline were relatively lower than those of other SBSEC isolates of a clinical origin. An investigation of the ARGs against those antimicrobials indicated that tetracycline resistance of SBSECs generally correlated with the presence of tet(M)-possessing Tn916-like transposon. However, no correlation between the presence of ARGs and phenotypic resistance to erythromycin and clindamycin was observed. Although a limited number of animals and their SBSEC isolates were examined, this study provides insights into the potential intraspecies biodiversity of ruminant-origin SBSEC and the current status on antimicrobial resistance of the bacteria in the Korean livestock industry.

scholarly journals Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 685-704 ◽  
Author(s):  
Kristiina Mark ◽  
Carolina Cornejo ◽  
Christine Keller ◽  
Daniela Flück ◽  
Christoph Scheidegger
Keyword(s):  
454 Pyrosequencing ◽  
Ecological Integrity ◽  
Common Species ◽  
Sequencing Error ◽  
Reference Database ◽  
Biological Sequence ◽  
Internal Transcribed Spacer Region ◽  
Epiphytic Lichen ◽  
Fungal Partner ◽  
A Genome

Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database—currently the most complete database for lichen-forming fungi—can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).

Cuticular disruption and mortality of Caenorhabditis elegans exposed to culture filtrate of Byssochlamys nivea Westling

Nematology ◽  
2001 ◽  
Vol 3 (4) ◽  
pp. 355-363 ◽  
Author(s):  
Ja-On Park ◽  
Krishnapillai Sivasithamparam ◽  
Emile Ghisalberti ◽  
Jaih Hargreaves ◽  
Walter Gams ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Culture Filtrate ◽  
Structural Changes ◽  
Phytophthora Cinnamomi ◽  
Pathogenic Fungi ◽  
Gaeumannomyces Graminis ◽  
Pythium Irregulare ◽  
Potato Dextrose Broth ◽  
C Elegans

AbstractA strain of a Byssochlamys nivea, isolated from saline mud in Western Australia as a part of statewide survey of soil fungi for nematophagous activity, was evaluated for its effect on nematodes. Culture filtrate of the fungus grown on potato dextrose broth for 7 days caused structural changes in the cuticle, aggregation of individuals, and mortality of Caenorhabditis elegans. In addition, the culture filtrate completely inhibited hatching of C. elegans eggs. Exudates from agar colonies also caused cuticular disruption and mortality of C. elegans. The cuticular disruption observed, not reported in nematodes before, was initiated in the labial region and spread towards the posterior region of the nematode within 10 min of application. This reaction occurred only in live nematodes. Cuticular disruption and mortality caused by the culture filtrate varied according to growth conditions. The active compound(s) in the culture filtrate were thermostable (100°C for 1 h); however freezing the culture filtrate (-20°C for 2 days) eliminated the activities, as did dialysis (<14 000 molecular weight). Cuticular disruption and mortality were also observed when the nematode was exposed to culture filtrates of two other strains of B. nivea supplied by CBS, The Netherlands. The culture filtrate also inhibited in vitro growth of the plant-pathogenic fungi Fusarium oxysporum, Gaeumannomyces graminis var. tritici, Phytophthora cinnamomi, Pythium irregulare and Rhizoctonia solani.

scholarly journals Characterization and Phylogeny of Fungi from Industrial Wastewater Using Highly Conserved Multiple Gene Loci

2021 ◽  
Author(s):  
Blessing Amaka Ezeonuegbu ◽  
Dauda Abdullahi Machido ◽  
Clement Z. Whong ◽  
Wisdom S. Japhet ◽  
Clement Ameh Yaro ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Industrial Effluent ◽  
Pcr Amplification ◽  
Morphological Characterization ◽  
Likelihood Method ◽  
Internal Transcribed Spacer Region ◽  
Fungal Isolates ◽  
Fungal Dna Extraction

Abstract The aim of this study was isolation and molecular characterization of fungi from untreated industrial effluent by multigene phylogenetic analyses. The Fungi isolated were characterized based on PCR amplification and genomic sequencing of the internal transcribed spacer region (ITS), partial β-tubulin (Ben A), calmodulin (CaM), and DNA-directed RNA polymerase second large subunit (RPB2) genes, along with morphological characterization and species diversity. Fungal DNA extraction kits and primers sets for the selected genes were purchased and used following the manufacturer’s instructions. The obtained sequences were subjected to BLAST analysis and the corresponding fungal isolates were assigned species names after comparison with representative sequences available in GenBank. All the sequences from this study were deposited in GenBank and the accession number assigned. Phylogenetic trees of the fungal isolates were drawn for each gene by the Maximum Likelihood method using MEGA 7.0 software. Fifteen (15) Fungi species belonging to four genera of Aspergillus, Penicillium, Fusarium and Trichoderma with Aspergillus as the predominant genus were identified.

scholarly journals Eutypa, Eutypella, and Cryptovalsa Species (Diatrypaceae) Associated with Prunus Species in South Africa

Plant Disease ◽  
2018 ◽  
Vol 102 (7) ◽  
pp. 1402-1409 ◽  
Author(s):  
Providence Moyo ◽  
Ulrike Damm ◽  
Lizel Mostert ◽  
Francois Halleen
Keyword(s):  
South Africa ◽  
Phylogenetic Analyses ◽  
Fruit Trees ◽  
Fungal Species ◽  
Stone Fruit ◽  
Prunus Species ◽  
Internal Transcribed Spacer Region ◽  
Eutypa Lata ◽  
Eutypa Dieback ◽  
Prunus Spp

Stone fruit trees (Prunus spp.) are economically important fruit trees cultivated in South Africa. These trees are often grown in close proximity to vineyards and are to a large extent affected by the same trunk disease pathogens as grapevines. The aim of the present study was to determine whether stone fruit trees are inhabited by Diatrypaceae species known from grapevines and whether these trees could act as alternative hosts for these fungal species. Isolations were carried out from symptomatic wood of Prunus species (almond, apricot, cherry, nectarine, peach, and plum) in stone fruit growing areas in South Africa. Identification of isolates was based on phylogenetic analyses of the internal transcribed spacer region and β-tubulin gene. Forty-six Diatrypaceae isolates were obtained from a total of 380 wood samples, from which five species were identified. All five species have also been associated with dieback of grapevine. The highest number of isolates was found on apricot followed by plum. No Diatrypaceae species were isolated from peach and nectarine. Eutypa lata was the dominant species isolated (26 isolates), followed by Cryptovalsa ampelina (7), Eutypa cremea (5), Eutypella citricola (5), and Eutypella microtheca (3). First reports from Prunus spp. are E. cremea, E. citricola, and E. microtheca. Pathogenicity tests conducted on apricot and plum revealed that all these species are pathogenic to these hosts, causing red-brown necrotic lesions like those typical of Eutypa dieback on apricot.

Amanita submelleialba sp. nov. in section Amanita from northern Thailand

Phytotaxa ◽  
2021 ◽  
Vol 513 (2) ◽  
pp. 129-140
Author(s):  
YUAN S. LIU ◽  
JIAN-KUI LIU ◽  
PETER E. MORTIMER ◽  
SAISAMORN LUMYONG
Keyword(s):  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Line Drawing ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Nuclear Rdna ◽  
Internal Transcribed Spacer Region ◽  
Northern Thailand ◽  
Extant Species ◽  
Distinct Lineage

Amanita submelleialba sp. nov. in section Amanita, is described from northern Thailand based on both multi-gene phylogenetic analysis and morphological evidences. It is characterized by having small to medium-sized basidiomata; a yellow to yellowish pale pileus covering pyramidal to subconical, white to yellow white volval remnants; globose stipe base covered conical, white to yellow white volval remnants; fugacious subapical annulus; and absent clamps. Multi-gene phylogenetic analyses based on partial nuclear rDNA internal transcribed spacer region (ITS), partial nuclear rDNA larger subunit region (nrLSU), RNA polymerase II second largest subunit (RPB2), partial translation elongation factor 1-alpha (TEF1-α) and beta-tubulin gene (TUB) indicated that A. submelleialba clustered together with A. elata and A. mira, but represented as a distinct lineage from other extant species in section Amanita. The detailed morphological characteristics, line-drawing illustration and comparisons with morphologically similar taxa are provided.

Geographically disjunct phylogenetic lineages in Leptogium hibernicum reveal Leptogium krogiae sp. nov. from East Africa

2017 ◽  
Vol 49 (3) ◽  
pp. 239-251
Author(s):  
Torbjørg BJELLAND ◽  
Mika BENDIKSBY ◽  
Andreas FRISCH
Keyword(s):  
East Africa ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Common Species ◽  
Montane Forests ◽  
Phylogenetic Lineages

AbstractPhylogenetic analyses of nuclear (Mcm7, nrITS, nrLSU) and mitochondrial (mrSSU) DNA sequences revealed geographically disjunct lineages in Leptogium hibernicum. One of these lineages is described here as Leptogium krogiae, which differs from L. hibernicum in the thinner thallus (190–210 µm vs. 390–480 µm), shallowly striate lobes instead of deeply furrowed lobes, isidia that are seldom distinctly flattened, and apothecia with a subhymenial euparaplectenchymatous layer. Leptogium krogiae is a widespread epiphyte in mist-affected woodlands and montane forests in East Africa and appears to be a common species.

A new Crocus L. (Iridaceae) species from SE Turkey, based on morphological and molecular data

Phytotaxa ◽  
2015 ◽  
Vol 239 (3) ◽  
pp. 223 ◽  
Author(s):  
Osman Erol ◽  
Doerte Harpke ◽  
Hasan Yıldırım
Keyword(s):  
Phylogenetic Analyses ◽  
Type Specimen ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Full Description ◽  
New Taxon ◽  
Internal Transcribed Spacer Region ◽  
Se Turkey

Crocus musagecitii is described as a new species. Diagnostic morphological characters, a full description and detailed illustrations are provided on the basis of the type specimen and wild specimens. Morphologically, C. musagecitii is close to Crocus biflorus subsp. pseudonubigena. Crocus musagecitii differs from C. biflorus subsp. pseudonubigena by the lack of stripes or narrow purplish tongue on outside of outer tepals, wider tepals, and homogenously yellow anthers. In order to clarify the phylogenetic position of this species within the Crocus adamii species complex, we sequenced the internal transcribed spacer region (ITS: ITS1 + 5.8SrDNA + ITS2) and 5’ external transcribed spacer (ETS) of the nuclear ribosomal DNA (rDNA). A phylogenetic tree obtained by Bayesian phylogenetic inference is given. Phylogenetic analyses revealed that the new taxon is close to C. munzurensis. Crocus musagecitii differs from its phylogenetically closest relative C. munzurensis by the corm tunics (C. musagecitii: coriaceus; C. munzurensis: membranous), the number of leaves (C. musagecitii: up to 8; C. munzurensis: up to 4) and non-hairy leaf margins.

scholarly journals Diversity of Diatrypaceae Species Associated with Dieback of Grapevines in South Africa, with the Description of Eutypa cremea sp. nov.

Plant Disease ◽  
2018 ◽  
Vol 102 (1) ◽  
pp. 220-230 ◽  
Author(s):  
Providence Moyo ◽  
Lizel Mostert ◽  
Christoffel F.J. Spies ◽  
Ulrike Damm ◽  
Francois Halleen
Keyword(s):  
South Africa ◽  
Cross Section ◽  
Internal Transcribed Spacer ◽  
Dominant Species ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Internal Transcribed Spacer Region ◽  
Canker Pathogen ◽  
Grapevine Canker ◽  
First Time

Recent studies in grape-growing areas including Australia, California, and Spain have revealed an extensive diversity of Diatrypaceae species on grapevines showing dieback symptoms and cankers. However, in South Africa, little is known regarding the diversity of these species in vineyards. The aim of this study was, therefore, to identify and characterize Diatrypaceae species associated with dieback symptoms of grapevine in South Africa. Isolates were collected from dying spurs of grapevines aged 4 to 8 years old, grapevine wood showing wedge-shaped necrosis when cut in cross section as well as from perithecia on dead grapevine wood. The collected isolates were identified based on morphological characters and phylogenetic analyses of the internal transcribed spacer region (ITS) and β-tubulin gene. Seven Diatrypaceae species were identified on grapevine, namely Cryptovalsa ampelina, C. rabenhorstii, Eutypa consobrina, E. lata, E. cremea sp. nov., Eutypella citricola, and E. microtheca. The dying spurs yielded the highest diversity of species when compared with the wedge-shaped necrosis and/or perithecia. C. ampelina was the dominant species in the dying spurs, followed by E. citricola, whereas E. lata was the dominant species isolated from the wedge-shaped necroses and perithecia. These results confirm E. lata as an important grapevine canker pathogen in South Africa, but the frequent association of C. ampelina with spur dieback suggests that this pathogen plays a more prominent role in dieback than previously assumed. In some cases, more than one species were isolated from a single symptom, which suggests that interactions may be occurring leading to decline of grapevines. C. rabenhorstii, E. consobrina, E. citricola, E. microtheca, and E. cremea are reported for the first time on grapevine in South Africa.

scholarly journals A new concept for Dictyostelium sphaerocephalum based on morphology and phylogenetic analysis of nuclear ribosomal internal transcribed spacer region sequences

2007 ◽  
Vol 85 (1) ◽  
pp. 104-110 ◽  
Author(s):  
Maria Romeralo ◽  
Omar Fiz-Palacios ◽  
Carlos Lado ◽  
James C. Cavender
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Morphological Plasticity ◽  
Branching Pattern ◽  
Classical Concept ◽  
Internal Transcribed Spacer Region

Three dictyostelid isolates were found in Spain and Argentina that are morphologically different from known species. These isolates have some features similar to Dictyostelium sphaerocephalum (Oudem.) Sacc., Marchal & É.J. Marchal, but differ in size and sorocarp branching pattern. We sequenced the nuclear ribosomal internal transcribed spacer region to explore phylogenetic relationships among this group of species, including the three new isolates and their closest relatives. In all phylogenetic analyses performed, sequences of all three isolates group together with sequences from “typical” D. sphaerocephalum samples. This result supports previous observations of the morphological plasticity in dictyostelids, especially D. sphaerocephalum, leading us to broaden the classical concept of this species.

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