Query: identification of fungal species for cultural characteristics pdf

title: Morphological Characterization and Molecular Identification of Stem end Rot Associated Fungal Species Isolated from 'Karutha Colomban' Mango Fruits in Sri Lanka
abstract: Stem End Rot (SER) is one of the most frequently found mango postharvest diseases in many countries including Sri Lanka. Availability of a significantly detailed study on morphological and molecular characterization of the SER associated fungal species is comparatively low. The present study has been carried out considering the above fact.  SER disease associated fungi were isolated and identification was carried out using morphological characteristics. Identification was confirmed by phylogenetic analysis of newly generated ITS sequencing data using Maximum Likelihood (ML) with RAxML software (Ver.8.2.10)  From the morphological studies it was observed that the fungal isolates SER1, SER2, SER3 and SER6 produced conidia on Potato Dextrose Agar. Both morphological and molecular results revealed that the isolates of SER1, SER4, SER5, and SER6 which were isolated from diseased Karutha Colomban mango fruits with SER (in Sri Lanka) belong to Lasiodiplodia sp. Nodulisporium sp. Xylaria feejeensis and Pestalotiopsis sp. respectively. Both SER2 and SER3 were confirmed as Phomopsis sp. During the present study two new fungal species (Xylaria spp. and Nodulisporium spp. were also identified for the first time from SER of Karutha Colomban mango fruits.  The pathogenicity of these isolates will be tested in near future, since the study was mainly focused on the isolation and identification of the SER associated fungal species.  Results of the present study will be very valuable for stakeholders in Agricultural sector, before designing control strategies at post harvest level in order to minimize the loss and extend the storage life of mango.

title: Study on the Identification of Fungal Pathogen Causing Yam Rot in Lesser Yam (Dioscorea esculenta) in Batticaloa District, Sri Lanka
abstract: Dioscorea esculenta commonly known as the lesser yam is cultivated in Batticaloa district of Sri Lanka a small scale. Pathogenic fungi reduce the quantity and quality of yam produced. Pathological investigations were carried out to find out the fungal organisms associated with yam rot of lesser yam. Eight pieces (2 mm in diameter) of the infected yam tissues were picked from the point of advancement of rot and inoculated on a solidified Potato Dextrose Agar (PDA) medium. Two replicates were made for each of the 4 yam tuber samples and the 8 plates were inoculated. The inoculated plates were incubated at room temperature (30degC) and observations were made daily for possible fungal growth. Sub culturing was done to obtain pure cultures of the isolates. Cultural characteristics of the fungi were observed and recorded. The identification of the isolates was done by examining the isolates macroscopically and microscopically. The causative fungal pathogen was identified as Fusarium solani (Mart. Sacc. based on the colony and microscopic characteristics of the pathogen. Fusarium solani produced white cream mycelia. Macroconidia are three to four septate, slightly curved, 28 42 x 4 6 um. Microconidia are abundant, cylindrical to oval, one to two celled, 8 16 x 2 4.5 um. Pathogenicity test carried out confirmed this fungal species as the pathological agent of the lesser yam rot. The finding of the causal organism of the yam rot disease would be very useful in choosing effective control measures to extend the life span of yam in storage.

title: 639. Performance Characteristics of an FDA Cleared Multiplex Panel for the Rapid Identification of Fungal Pathogens From Positive Blood Culture
abstract: Routine identification of fungal pathogens from positive blood cultures by conventional culture based methods can be time consuming, delaying effective treatment of appropriate antifungal agents. The GenMark Dx ePlex(r) Investigational Use Only Blood Culture Identification Fungal Pathogen Panel (BCID FP) was assessed in a multicenter study to determine the performance of all 15 fungal targets on the BCID FP sample to answer cartridge, which incorporates extraction, amplification, digestion, hybridization and detection using GenMark eSensor(r) technology, in approximately 100 minutes.  Ten sites across the United States collected samples that were tested at 4 clinical sites comparing the BCID FP to traditional culture, MALDI TOF MS, microbiological and biochemical techniques. Discrepant results were analyzed by a bi directional PCR/sequencing directly in residual blood culture samples. Sensitivity and specificity were determined for each fungal target.  A total of 725 contrived samples along with 120 retrospective and 21 prospective collected (fresh/frozen) clinical samples were tested with the BCID FP. Of the 11 Candida species on the panel (C. albicans, C. auris, C. dubliniensis, C. famata, C. glabrata, C. guilliermondii, C. kefyr, C. krusei, C. lusitaniae, C. parapsilosis, and C. tropicalis) sensitivity and specificity ranged from 97.1 to 100% and 99.8 to 100% respectively. For the other organisms detected on the panel, sensitivity and specificity were 100% for both Cryptococcus neoformans and C. gattii. Sensitivity and specificity for Fusarium sp. and Rhodotorula sp. were 98.6% and 100% and 96.2% and 99.9% respectively. In 4 of the 141 clinical samples, the ePlex BCID FP panel correctly identified an additional Candida species that was undetected by traditional methods.  The ePlex BCID FP panel offers a faster turnaround time than a standard of care methods for the detection of important fungal pathogens in positive blood cultures in a time frame that may allow for earlier antifungal interventions. The BCID FP panel also is the only FDA cleared panel available to date containing the highly anti fungal drug resistant C. auris target.  No reported disclosures.

title: Isolation and Morphological Identification of Culturable Endophytic Fungal Species from Mangrove Ecosystem
abstract: Endophytic fungi inhabit healthy plant tissues, and are now considered as ubiquitous symbionts of plants. Besides having the positive effects on the plants in phytostimulation, production of pigments, enzymes and bioactive compounds and nutrient cycling, they are also responsible for the destruction of host tissues and toxic production within the host. The endophytic fungi can be found in any part of the plant such as scale primordial, meristem, resin ducts, petiole, buds, stem, root, shoot, leaves, barks and even in the pneumatophores. Mangroves act as a host for plenty of endophytic fungal populations. The endophytic fungi obtained from mangroves have certain specialized characteristics and are resistant to several environmental stress conditions. Aim of the present study is to isolate and identify endophytic fungi inhabiting mangrove plant species that are abundantly found along the state of Northern Kerala, India. The collected plant specimens were surface sterilized and ground to paste form to earn the extract, which was then inoculated into the medium to obtain fungal culture. Among seven plant specimens collected, six types of endophytic fungi were morphologically identified as Aspergillus sp. (two different species) Penicillium sp. Alternaria sp. Fusarium sp. and Sarocladium sp.

title: Exserohilum keratitis: Clinical profile of nine patients and comparison of morphology versus ITS Based DNA sequencing for species identification of the fungal isolates
abstract: The objective of this study was to describe the microbiological and clinical features of nine cases of Exserohilum keratitis.  Fungal isolates from corneal scrapings were identified based on macroscopic and microscopic characteristics of the colonies and DNA sequencing of ITS1 5.8S ITS2 region in the rRNA gene. All patients were treated with topical and if required systemic antifungals. Therapeutic penetrating keratoplasty (TPK) was done in case of failed medical therapy.  Morphologically, all fungal isolates were Exserohilum rostratum except one Exserohilum mcginnisii. Based on the BLAST analysis, 6 isolates showed 100% similarity to Setosphaeria rostrata (CBS 112815) and E. mcginnisii (CBS 20308) The other three isolates were Setosphaeria holmii (CBS 128053) not reported earlier in fungal keratitis. Three patients were lost to follow up and response to medical therapy was good (Healed scar 4 patients) Two out of nine patients were advised TPK.  Diagnosis and clinical features of Exserohilum keratitis are akin to other dematiaceous keratitis. The two morphological species of E. mcginnisii and E. rostratum are indistinguishable from Setosphaeria rostratum at DNA sequence level, which justifies the retention of the latter nomenclature.

title: Electrochemical identification of toxigenic fungal species using solid state voltammetry strategies.
abstract: An electrochemical methodology for the characterization of mycotoxin producing fungal species from the genera Aspergillus and Fusarium using solid state voltammetry is described. Upon attachment of fungal colony microsamples to glassy carbon electrodes in contact with aqueous acetate buffer, characteristic voltammetric signals mainly associated to the oxidation of polyphenolic metabolites are recorded. The possibility of fungi localized electrochemical processes was assessed by means of electron microscopy and field emission scanning electrochemical microscopy coupled to the application of oxidative potential inputs. Using pattern recognition methods, the determined voltammetric profiles were able to discriminate between mycotoxin producing fungi from different sections and to identify selected toxigenic species of the Aspergillus and Fusarium genera isolated from grapes and cereals.

title: Identification of drivers of landscape distribution of forest orchids using germination experiment and species distribution models
abstract: The family of orchids involves a number of critically endangered species. Understanding of drivers of their landscape distribution could provide a valuable insight into their decline. Our objectives were to develop models predicting distribution of selected orchid species four co occurring forest orchid species, Cephalanthera rubra, Epipactis atrorubens, E. helleborine, and Neottia nidus avis at a landscape scale using a wide range of habitat characteristics. Subsequently, we compared the model predictions with species occurrence and the results of the field germination experiment while considering two germination stages asymbiotic (early stage) and symbiotic. And finally, we attempted to identify possible drivers of species' landscape distribution (i.e. dispersal, availability of habitat patches, or fungal associates) We have discovered that different habitat characteristics determined the distribution of different orchids. The species also differed in terms of availability of suitable habitat patches and patch occupancy (the highest being E. atrorubens with 80% Landscape distribution of the species was primarily restricted by the availability of fungal associates (the most important factor for C. rubra) and by the availability of suitable habitat patches (the most important in case of N. nidus avis) Despite expected easy dispersal of spores, orchid distribution seems to be limited by the availability of fungal associates in the landscape. In contrast, the availability of orchid seeds does not seem to limit their distribution. These results can provide useful guidelines for conservation of the studied species.

title: First identification of long non coding RNAs in fungal parasite Nosema ceranae
abstract: Nosema ceranae is a unicellular fungal parasite of honey bees and causes huge losses for apiculture. Until present, no study on N. ceranae long non coding RNAs (lncRNAs) was documented. Here, we sequenced purified spores of N. ceranae using strand specific library construction and high throughput RNA sequencing technologies. In total, 83 novel lncRNAs were predicted from N. ceranae spore samples, including lncRNAs, long intergenic non coding RNAs (lincRNAs) and sense lncRNAs. Moreover, these lncRNAs share similar characteristics with those identified in mammals and plants, such as shorter length and fewer exon number and transcript isoforms than protein coding genes. Finally, the expression of 12 lncRNAs was confirmed with RT PCR, confirming their true existence. To our knowledge, this is the first evidence of lncRNAs produced by a microsporidia species, offering novel insights into basic biology such as regulation of gene expression of this widespread taxonomic group.

title: Species identification of dermatophytes isolated from human superficial fungal infections by conventional and molecular methods
abstract: Dermatophyte identification is based on the detection of fungal elements by direct microscopy of clinical specimens combined with culture based full identification. Phenotypic identification includes macromorphological, micromorphological, and physiological characteristics of the colonies. In the last few years, molecular approaches have been proven to be useful for identification of dermatophyte species.  To investigate the conventional and molecular methods used for identification of dermatophytes.  Fifty five specimens collected from human dermatophytosis cases were subjected to mycological examination. Isolated dermatophytes were identified by phenotypic methods. Molecular identification was done using PCR amplification of internal transcribed spacer (ITS1 and ITS4) followed by restriction fragment length polymorphism using the restriction endonuclease enzyme MvaI, application of PCR using single repetitive oligonucleotide (GACA)4] and DNA sequencing.  The obtained dermatophyte isolates (n=48) identified by phenotypic methods were as follows: 15 Microsporum canis, 12 Trichophyton violaceum, 12 Trichophyton rubrum, 5 Epidermophyton floccosum, and 4 Trichophyton mentagrophytes. However, restriction fragment length polymorphism using MvaI and repetitive (GACA)4 molecular methods identified 19 dermatophyte isolates identical to those classified by phenotypic methods. DNA sequencing reidentified one isolate formerly determined to be T. rubrum into Trichophyton raubitschekii.  Although the molecular method is rapid and represents technological advancement in the identification of dermatophytes, it is too expensive to be used as a routine method and needs more effort. We recommend its use in the absence of skilled mycologists or in atypical and variants of dermatophytes.

title: Molecular and morphological identification of fungal species isolated from rice meju
abstract: The microflora of natural fermented Korean rice meju are assumed to be diverse, but has not yet been investigated. The fungi was isolated and identified from rice meju on the bases of morphology, culture characteristics, and molecular approaches of internal transcribed spacer and b tubulin gene sequencing, and their enzyme activities were determined. Six species of fungi were primarily isolated from rice meju, specifically Aspergillus candidus, Aspergillus tritici, Cladosporium oxysporum, Penicillium commune, Penicillium griseofulvum, and Rhizomucor variabilis var. regularior. All isolates produced protease (5.17 15.78) and all strains except Mucor circinelloides PR06 expressed amylase activities (0.04 0.23) In comparison, lipase was produced by zygomycetous fungi isolates (1.70 0.25) and Aspergillus oryzae PR07 (0.68) The enzyme producing fungal strains might be involved in the rice meju fermentation. The identification of fungal diversity in meju is useful for understanding the fermentation processes and these strains might be used in the fermentation of foods.