scholarly journals Species Identification in Plant-Associated Prokaryotes and Fungi Using DNA

2020 ◽  
Vol 4 (2) ◽  
pp. 103-114 ◽  
Author(s):  
Patrik Inderbitzin ◽  
Barbara Robbertse ◽  
Conrad L. Schoch
Keyword(s):  
Microbial Diversity ◽  
Species Identification ◽  
Fungal Species ◽  
Biological Information ◽  
Fungal Taxonomy ◽  
Fungal Organisms

Species names are fundamental to managing biological information. The surge of interest in microbial diversity has resulted in an increase in the number of microbes that need to be identified and assigned a species name. This article provides an introduction to the principles of DNA-based identification of Archaea and Bacteria traditionally known as prokaryotes, and Fungi, the Oomycetes and other protists, collectively referred to as fungi. The prokaryotes and fungi are the most commonly studied microbes from plants, and we introduce the most relevant concepts of prokaryote and fungal taxonomy and nomenclature. We first explain how prokaryote and fungal species are defined, delimited, and named, and then summarize the criteria and methods used to identify prokaryote and fungal organisms to species.

scholarly journals Differences in Microbial Community and Metabolites in Litter Layer of Plantation and Original Korean Pine Forests in North Temperate Zone

2020 ◽  
Vol 8 (12) ◽  
pp. 2023
Author(s):  
Yue Wang ◽  
Ting Li ◽  
Chongwei Li ◽  
Fuqiang Song
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Bacterial Species ◽  
Fungal Species ◽  
Pine Forest ◽  
Korean Pine ◽  
Litter Layer ◽  
Pine Plantation ◽  
Korean Pine Forest ◽  
Korean Pine Plantation

In order to explore the relationship between microbial diversity and metabolites in the litter layer of northern temperate forests, the microbial community structure and metabolite species in the litter layer of an original Korean pine forest and Korean pine plantation of northern temperate climate were determined on the basis of high-throughput sequencing and metabonomic techniques. The results showed that there were 698 bacterial genera and 363 fungal genera in the litter samples in the original Korean pine forest. Linear discriminant effect size (LEfSe) analysis showed that there were 35 indicator bacterial species and 19 indicator fungal species. In the litter samples of the Korean pine plantation, there were 622 bacterial genera and 343 fungal genera. Additionally, LEfSe analysis showed that there were 18 indicator bacterial species and 5 indicator fungal species. The litter of the two forest types contained 285 kinds of organic compounds, among which 16 different metabolites were screened, including 6 kinds of organic acids, 5 kinds of amino acids, 2 kinds of sugars, 2 kinds of sugar alcohols, and 1 kind of lipid. Latescibacteria, Rokubacteria, and Olpidiomycota are unique to the original Korean pine forest. They can catalyze the degradation rate of litter and decompose cellulose and chitin, respectively. Subgroup 6 was abundant in the lower litter layer. Subgroup 6 can grow with carbon compounds as substrate. It was clear that the microbial diversity of the litter layer in the original Korean pine forest was higher than that of the Korean pine plantation. Moreover, whether original forest or plantation forest, the lower-litter layer microbial diversity was higher than that in the middle-litter layer. CCA showed that the main metabolites were related to Chitinophagaceae_uncultured were saccharopine. The main metabolites associated with Mortierella and Polyscytalum were myo-inositol. At the same time, analysis of the difference between the litter layer of the original Korean pine forest and the Korean pine plantation also provides a theoretical basis for their participation in the element cycles of forest ecosystems.

scholarly journals Phylogenetic Analysis of Polyporous Fungi Collected from Batam Botanical Garden, Riau Province, Indonesia

2018 ◽  
Vol 10 (3) ◽  
pp. 510-518 ◽  
Author(s):  
Anis Sri Lestari ◽  
Deni Zulfiana ◽  
Apriwi Zulfitri ◽  
Ni Putu Ratna Ayu Krishanti ◽  
Titik Kartika
Keyword(s):  
Botanical Garden ◽  
Morphological Characters ◽  
Fungal Species ◽  
Vital Role ◽  
Pycnoporus Sanguineus ◽  
Dead Trees ◽  
Lenzites Betulina ◽  
Fungal Organisms ◽  
Advance Research ◽  
Fungal Tissue

Botanical gardens are areas that provide protection for trees and other organisms like polyporous fungi. Polyporous fungi are important fungi that degrade remaining lignocellulosic in leaf litter or dead trees. These mycobiota are also noted for their vital role in biorefinery, bioremediation, medicine and phytopathogen. The knowledge of the importance of the polyporous fungi to describe polyporous fungal species is fundamental for generating data base information of their occurrence and their functions. This research’s goal was to explore and characterize the polyporous fungi collected in Batam Botanical Garden in three sampling areas. Fungal samples were collected in May and July 2017. Subsequently, morphological characters were recorded, the fungal tissue was isolated to extract the DNA, then the data sequence was amplified and aligned to construct a phylogenetic tree. Five fungal families found belong to order Polyporales and were classified morphologically. They were Polyporaceae, Ganodermataceae, Fomitopsidaceae, Irpicaceae and Hymenochaetaceae. Three fungal species namely; Pycnoporus sanguineus, Trametes ijubarskii, and Antrodia wangii were identified based on phyllogenetic analysis whereas seven other fungal samples were identified as Earliella scabrosa, Hexagonia tenuis, Polyporus tenuiculus Lenzites betulina, Lentinus concavus, Phellinus rimosus and Hexagonia apiaria. This study classifies and adds fundamental databases on fungal taxonomy and diversity on the fungal organisms found in Batam Botanical Garden. This background data is vital to carry out an advance research in some areas such as bio-chemistry, bio-degradation, pharmacology and biotechnology.

scholarly journals Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico

2019 ◽  
Author(s):  
Carolina Rocha-Arriaga ◽  
Annie Espinal-Centeno ◽  
Shamayim Martinez-Sanchez ◽  
Juan Caballero-Pérez ◽  
Luis D. Alcaraz ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Fermentation Process ◽  
Alcoholic Beverage ◽  
Essential Amino Acids ◽  
Fungal Species ◽  
Rrna Gene ◽  
List Type ◽  
Community Profiling ◽  
Massive Sequencing ◽  
Carl Von Linné

AbstractSome of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey. This was changed again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as crops, but also part of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli. This beverage represents a precolumbian biotechnological development obtained by the natural fermentation of the mead (aguamiel) from such plants. The pulque played a central role in mexican prehispanic cultures, mainly the Mexica and the Tolteca, where it was considered as sacred. For modern Mexicans, pulque is still part of their heritage and, in recent times, there has been a renewed interest in this ancient beverage, due to its high content in nutrients such as essential amino acids. We focus this study in the microbial diversity involved in pulque fermentation process, specially because it is still produced using classic antique technologies,. In this work, we report the microbiome of pulque fermentation stages, using massive sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) for describing bacterial and fungal diversity and dynamics along pulque production. In this study, we are providing the most diverse catalogue of microbes during pulque production with 57 identified bacterial genus and 94 fungal species, these findings allowed us to identify core microbes resilient during pulque production which point to be potential biomarkers exclusive to each fermentation stage.Our approach allowed the identification of a broader microbial diversity in PulqueWe increased 4.4 times bacteria genera and 40 times fungal species detected in mead.Newly reported bacteria genera and fungal species associated to Pulque fermentation

scholarly journals Microbial Diversity in the Phyllosphere and Rhizosphere of an Apple Orchard Managed under Prolonged “Natural Farming” Practices

2021 ◽  
Vol 9 (10) ◽  
pp. 2056
Author(s):  
Ying-Hong He ◽  
Charith Raj Adkar-Purushothama ◽  
Tsutae Ito ◽  
Asuka Shirakawa ◽  
Hideki Yamamoto ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Fungal Species ◽  
Apple Orchard ◽  
Disease Suppression ◽  
Farming Practices ◽  
Main Determinant ◽  
Metagenome Analysis ◽  
Factors Analysis ◽  
Natural Farming

Microbial diversity in an apple orchard cultivated with natural farming practices for over 30 years was compared with conventionally farmed orchards to analyze differences in disease suppression. In this long-term naturally farmed orchard, major apple diseases were more severe than in conventional orchards but milder than in a short-term natural farming orchard. Among major fungal species in the phyllosphere, we found that Aureobasidium pullulans and Cryptococcus victoriae were significantly less abundant in long-term natural farming, while Cladosporium tenuissimum predominated. However, diversity of fungal species in the phyllosphere was not necessarily the main determinant in the disease suppression observed in natural farming; instead, the maintenance of a balanced, constant selection of fungal species under a suitable predominant species such as C. tenuissimum seemed to be the important factors. Analysis of bacteria in the phyllosphere revealed Pseudomonas graminis, a potential inducer of plant defenses, predominated in long-term natural farming in August. Rhizosphere metagenome analysis showed that Cordyceps and Arthrobotrys, fungal genera are known to include insect- or nematode-infecting species, were found only in long-term natural farming. Among soil bacteria, the genus Nitrospira was most abundant, and its level in long-term natural farming was more than double that in the conventionally farmed orchard.

Panfungal PCR assays using fresh frozen paraffin embedded tissue specimens for fungal species identification and the detection of azole-resistance mutations in the A. fumigatus cyp51A gene at a South Korean hospital

2019 ◽  
Author(s):  
In Young Jung ◽  
Youn-Jung Lee ◽  
Hyo Sup Shim ◽  
Woon Ji Lee ◽  
Jun Hyoung Kim ◽  
...  
Keyword(s):  
Species Identification ◽  
Fungal Species ◽  
Azole Resistance ◽  
Histopathological Diagnosis ◽  
Resistance Mutations ◽  
South Korean ◽  
Ffpe Samples ◽  
Fungal Dna ◽  
Pcr Assays ◽  
Panfungal Pcr

Abstract Background: With rising concerns about changing fungal epidemiology and azole resistance in Aspergillus species, identifying fungal species and susceptibility patterns of mucorales and aspergillosis are crucial in the management of these diseases. The objectives of this study were to evaluate performance of panfungal PCR assays on formalin-fixed paraffin embedded (FFPE) samples for fungal species identification, and the detection of azole-resistance mutations in the Aspergillus fumigatus ( A.fumigatus ) cyp51A gene at a South Korean hospital. Methods: A total of 75 FFPE specimens with a histopathological diagnosis of aspergillosis or mucormycosis were identified during the 10-year study period (2006-2015). After deparaffinization and DNA extraction, panfungal PCR assays were conducted on FFPE samples for fungal species identification. The identified fungal species were compared with histopathological diagnosis. On samples identified as A.fumigatus , sequencings to identify frequent mutations in the cyp51A gene (tandem repeat 46 [TR46], L98H, and M220 alterations) that confer azole resistance were performed. Results: Specific fungal DNA was identified in 31 (41.3%) FFPE samples, and of these, 16 samples of specific fungal DNA were in accord with histopathological diagnosis of aspergillosis or mucormycosis. 15 samples had discordant histopathology and PCR results. No azole-mediating cyp51A gene mutation was revealed among nine cases of A. fumigatus . Moreover, no cyp51A mutations were identified among three cases with history of prior azole use. Conclusion: The pan-fungal PCR assay with FFPE sample may provide additional information on fungal species identification. No azole-resistance mediating mutations in the A. fumigatus cyp51A gene were identified among FFPE samples during study period.

scholarly journals Fungemia Surveillance in Denmark Demonstrates Emergence of Non-albicans Candida Species and Higher Antifungal Usage and Resistance Rates than in Other Nations

2018 ◽  
Vol 56 (4) ◽  
pp. e01907-17 ◽  
Author(s):  
Mariana Castanheira
Keyword(s):  
Candida Albicans ◽  
Candida Species ◽  
Susceptibility Testing ◽  
Antifungal Susceptibility ◽  
Fungal Species ◽  
Azole Resistance ◽  
Content Type ◽  
Fungal Organisms ◽  
Echinocandin Resistance ◽  
Resistance Rates

ABSTRACT Recent changes in the occurrence of fungal species and the difficulties in performing reference antifungal susceptibility testing highlight the importance of surveillance of fungal organisms and antifungal resistance rates. K. M. T. Astvad et al. report results from recent (2012 to 2015) fungemia surveillance in Denmark and compare the results to previous data (2004 to 2011), showing a decrease in Candida albicans infections accompanied by an increase in C. glabrata and C. dubliniensis infections (J Clin Microbiol 56:e01564-17, 2018, https://doi.org/10.1128/JCM.01564-17). Azole resistance among C. tropicalis and C. parapsilosis isolates and echinocandin resistance in C. krusei isolates were higher in Denmark than in other regions. Interestingly, the usage of antifungals is higher in Denmark than in other Nordic countries.

scholarly journals Pushing the Limits of MALDI-TOF Mass Spectrometry: Beyond Fungal Species Identification

2015 ◽  
Vol 1 (3) ◽  
pp. 367-383 ◽  
Author(s):  
Cosmeri Rizzato ◽  
Lisa Lombardi ◽  
Marina Zoppo ◽  
Antonella Lupetti ◽  
Arianna Tavanti
Keyword(s):  
Mass Spectrometry ◽  
Species Identification ◽  
Fungal Species ◽  
Maldi Tof Mass Spectrometry ◽  
Maldi Tof

scholarly journals Quantitative analysis of spore shapes improves identification of fungi

2021 ◽  
Author(s):  
Alexander Ordynets ◽  
Sarah Keßler ◽  
Ewald Langer
Keyword(s):  
Species Identification ◽  
Shape Analysis ◽  
Fungal Spores ◽  
Principal Component ◽  
Fungal Spore ◽  
Fungal Species ◽  
Automated Identification ◽  
Linear Measurements ◽  
Shape Information ◽  
Identification Of Fungi

Morphology of organisms is an important source of evidence for biodiversity assessment, taxonomic decisions, and understanding of evolution. Shape information about zoological and botanical objects is often treated quantitatively and in this form improves species identification. In studies of fungi, quantitative shape analysis was almost ignored. The disseminated propagules of fungi, the spores, are crucial for their taxonomy – currently in the form of linear measurements or subjectively defined shape categories. It remains unclear how much quantifying spore shape information can improve species identification. In this study, we tested the hypothesis that shape, as a richer source of information, overperforms size when performing automated identification of fungal species. We used the fungi of the genus Subulicystidium (Agaricomycetes, Basidiomycota) as a study object. We analysed 2D spore shape data via elliptic Fourier and Principal Component analyses. With flexible discriminant analysis, we achieved a slightly higher species identification success rate for shape predictors (61.5%) than for size predictors (59.1%). However, we achieved the highest rate for a combination of both (64.7%). We conclude that quantifying fungal spore shapes is worth the effort. We provide an open access protocol which, we hope, will stimulate a broader use of quantitative shape analysis in fungal taxonomy. We also discuss the challenges of such analyses that are specific to fungal spores.

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