DNA barcoding in Mucorales: an inventory of biodiversity

Absidia healeyae: a new species of Absidia (Mucorales) isolated from Victoria, Australia

Absidia healeyae is a new species described in the Mucorales genus Absidia after screening 16 strains of Absidia isolated from seven locations in the state of Victoria in Australia. After initial analysis of the large ribosomal subunit sequence, the genomes of representative strains from two clades were sequenced using short paired-reads. Additional taxonomic markers extracted from the genome sequencing data support the novelty of A. healeyae. The identification of a new species in the genus Absidia, from a relatively small collection of isolates, hints at an unexplored diversity in the early diverging lineages of fungi in Australia.

Intraspecific variability in cardinal growth temperatures and water activities within a large diversity of Penicillium roqueforti strains

Different strains of a given fungal species may display heterogeneous growth behavior in response to environmental factors. In predictive mycology, the consideration of such variability during data collection could improve the robustness of predictive models. Among food-borne fungi, Penicillium roqueforti is a major food spoiler species which is also used as a ripening culture for blue cheese manufacturing. In the present study, we investigated the intraspecific variability of cardinal temperatures and water activities (a_w), namely, minimal (T_min and a_wmin), optimal (T_opt and a_wopt) and maximal (T_max) temperatures and/or a_w estimated with the cardinal model for radial growth, of 29 Penicillium roqueforti strains belonging to 3 genetically distinct populations. The mean values of cardinal temperatures and a_w for radial growth varied significantly across the tested strains, except for T_max which was constant. In addition, the relationship between the intraspecific variability of the biological response to temperature and a_w and putative genetic populations (based on microsatellite markers) within the selected P. roqueforti strains was investigated. Even though no clear relationship was identified between growth parameters and ecological characteristics, PCA confirmed that certain strains had marginal growth response to temperature or a_w. Overall, the present data support the idea that a better knowledge of the response to abiotic factors such as temperature and a_w at an intraspecific level would be useful to model fungal growth in predictive mycology approaches.

First Report of Mucor irregularis Causing Postharvest Fruit Rot on Garcinia mangostana in China

Mangosteen (Garcinia mangostana Linn.) is an evergreen fruit tree grown in Southeast Asia. The fruit of Mangosteen is dark purple spherical with a diameter of 5 to 8 centimeter, a hard rind and white flesh. The seeds and pericarps of the fruit have long been utilized as a traditional medicine in Southeast Asia (Ovalle-Magallanes et al. 2017). Surveys were conducted during the months from March to April 2019 of fruit markets located in Wujing Town, Shanghai (31°02'33″ N, 121°28'04″ E), one noteworthy postharvest disease was observed. Overall 116 fruit samples were collected from 5 different supermarkets, 10.3% (12) of the fruits were found infected with the same symptoms during cold storage. The infected fruits were subjected to pathogen isolation and characterization. The junction areas between diseased and healthy tissues were cut into small pieces of diameter 5 mm, which were surface sterilized with 0.5% NaClO solution for 3 min, followed by rinsing in sterile water thrice, and then the tissues were placed on sterilized potato dextrose agar (PDA) plates supplemented with 50 μg/ml streptomycin. The colony edges of resulted fungal cultures were cut and removed to new PDA plates for purification after 2 days incubation at 28°C. After 3 rounds of subculture, a total of 19 purified isolates were obtained and these isolates showed similar phenotypes in morphological characters. The fungal colonies were fast growing (25 mm per day at 28°C on PDA plates) and were circular shaped with massive aerial hyphae, white to ochraceous color. Non-septate hyphae were hyaline and the septa were found only at the branching points. Sporangiophores arose from hyphae or from stolons. Sporangiospores were hyaline, smooth-walled, mostly subspherical to ellipsoidal, and measured 1.34 to 2.73 µm (width) and 3.12 to 6.19 µm (length) (1.98 ± 0.36×4.46 ± 0.69, n=100)(Alvarez et al. 2011). Three independent isolates (GM-07, GM-16, GM-19) were selected used for further genetic analysis and pathogenicity test. The internal transcribed spacer (ITS) and the D1/D2 region of the nuclear large subunit ribosomal RNA gene (LSU) were amplified by primers ITS1/ITS4 and primers NL1/LR3, respectively (Walther et al. 2013). BLASTn analyses of ITS (MN081612, MN081613, MN087659) and LUS (MN080423, MN080422, MN080432) sequences exhibited 99 to 100% identify to Mucor irregularis strains HZ640, extr25 and CBS977.68 (Accession numbers KC461926, MH510278 of ITS and JX976214 of LUS). These observed morphological features and molecular identification indicated that the pathogen possessed identical characteristics as Mucor irregularis Stchigel, Cano, Guarro & Ed. Alvarez (Alvarez et al. 2011). To conduct a pathogenicity test (Al-Sadi et al. 2014), 20 µl of spore suspension (106 spores ml-1) were inoculated into five healthy mangosteen fruits by sterile syringes, meanwhile another five healthy fruits were injected with sterilized water as controls. All inoculated fruits were kept in sealed plastic boxes at 28°C with a 12L/12D illumination cycle and 90% relative humidity. After about 3 to 7 days, the inoculated materials showed similar symptoms to those on the original diseased fruits, while control samples remained symptomless. M. irregularis was successfully re-isolated from symptomatic fruits, fulfilling Koch's postulates. Only three plant species that can be infected by M. irregularis have been reported so far, including key lime from Oman (Al-Sadi et al. 2014), corn from China (Peng et al. 2015), and sorghum from Brazil (Lima et al. 2018). To our knowledge, this is the first report of M. irregularis causing the postharvest rot on mangosteen fruit in China.

Cunninghamella arunalokei a New Species of Cunninghamella from India Causing Disease in an Immunocompetent Individual

Mucormycosis due to Cunninghamella spp. is a rare disease, especially in immunocompetent individuals. Here, we describe the isolation and characterization of a new species of Cunninghamella, causing chronic rhino-orbital-cerebral disease, and review cases of mucormycosis due to Cunninghamella spp. in immunocompetent individuals. The Basic Local Alignment Search Tool (BLAST) analysis of the internal transcribed spacer region (ITS) sequence of isolate NCCPF 890012 showed 90% similarity with Cunninghamella bigelovii, while the large ribosomal subunit (28S) and translation elongation factor-1 alpha (EF-1 alpha) gene sequences showed 98% identity. Further, the phylogenetic analysis with concatenated sequences clustered isolate (NCCPF 890012) closely with C. bigelovii. The ITS sequence showed the maximum variation among three genes analyzed and helped in the new species’ delineation. Comparison of the assembled whole genome of NCCPF 890012 with other Mucorales using 123 single-copy orthologous genes showed clustering within the genus Cunninghamella. Based on these findings, the isolate is considered to be a new species of Cunninghamella and designated as Cunninghamella arunalokei sp. nov. Despite repeated debridement and antifungal treatment, the patient had multiple recurrences with intracranial extension and succumbed to the illness.

Emergence of resistant Candida glabrata in Germany

Background

Candida glabrata is the second leading fungal pathogen causing candidaemia and invasive candidiasis in Europe. This yeast is recognized for its rapid ability to acquire antifungal drug resistance.

Objectives

We systematically evaluated 176 C. glabrata isolates submitted to the German National Reference Center for Invasive Fungal Infections (NRZMyk) between 2015 and 2019 with regard to echinocandin and fluconazole susceptibility.

Methods

Susceptibility testing was performed using a reference protocol (EUCAST) and a range of commercial assays. Hot spot regions of the echinocandin target FKS genes were sequenced using Sanger sequencing.

Results

In total, 84 of 176 isolates were initially classified as anidulafungin-resistant based on EUCAST testing. Of those, 71 harboured mutations in the glucan synthase encoding FKS genes (13% in FKS1, 87% in FKS2). Significant differences in anidulafungin MICs were found between distinct mutation sites. 11 FKS wild-type (WT) isolates initially classified as resistant exhibited anidulafungin MICs fluctuating around the interpretation breakpoint upon re-testing with multiple assays. Two FKS WT isolates consistently showed high anidulafungin MICs and thus must be considered resistant despite the absence of target gene mutations. Over one-third of echinocandin-resistant strains displayed concomitant fluconazole resistance. Of those, isolates linked to bloodstream infection carrying a change at Ser-663 were associated with adverse clinical outcome.

Conclusions

Resistant C. glabrata strains are emerging in Germany. Phenotypic echinocandin testing can result in misclassification of susceptible strains. FKS genotyping aids in detecting these strains, however, echinocandin resistance may occur despite a wild-type FKS genotype.

Discovery of Novel Backusella (Backusellaceae, Mucorales) Isolated from Invertebrates and Toads in Cheongyang, Korea

Three novel fungal species, Backusella chlamydospora sp. nov., B. koreana sp. nov., and B. thermophila sp. nov., as well as two new records, B. oblongielliptica and B. oblongispora, were found in Cheongyang, Korea, during an investigation of fungal species from invertebrates and toads. All species are described here using morphological characters and sequence data from internal transcribed spacer sequences of ribosomal DNA and large subunit of the ribosomal DNA. Backusella chlamydospora is different from other Backusella species by producing chlamydospores. Backusella koreana can be distinguished from other Backusella species by producing abundant yeast-like cells. Backusella thermophila is characterized by a variable (subglobose to oblong, applanate to oval, conical and ellipsoidal to pyriform) columellae and grows well at 37 °C. Multigene phylogenetic analyses of the combined ITS and LSU rDNA sequences data generated from maximum likelihood and MrBayes analyses indicate that B. chlamydospora, B. koreana, and B. thermophila form distinct lineages in the family Backusellaceae. Detailed descriptions, illustrations, phylogenetic tree, and taxonomic key to the Backusella species present in Korea are provided.

Diversity of Backusella (Mucoromycotina) in south-eastern Australia revealed through polyphasic taxonomy

Here we explore the diversity of one morphologically distinguishable genus in the Mucoromycotina, Backusella, in south-eastern Australia. We isolated more than 200 strains from locations across the states of Victoria and Tasmania. Characterization of these strains using a combination of approaches including morphology, sucrose utilization and whole genome sequencing for 13 strains, revealed 10 new species. The genetic basis for interspecies variation in sucrose utilization was found to be the presence of a gene encoding an invertase enzyme. The genus Backusella is revised and a new key for species identification produced. Given that we have more than doubled the number of species in this genus, this work demonstrates that there may be considerable undiscovered species diversity in the early diverging fungal lineages. Citation: Urquhart AS, Douch JK, Heafield TA, et al. 2021. Diversity of Backusella (Mucoromycotina) in south-eastern Australia revealed through polyphasic taxonomy. Persoonia 46: 1-25. https://doi.org/10.3767/persoonia.2021.46.01.

Endophytic fungus Mucor circinelloides DF20 promote tanshinone biosynthesis and accumulation in Salvia miltiorrhiza root

As a traditional Chinese medicine, Salvia miltiorrhiza rhizome is mainly used to treat cardiovascular diseases. Symbiosis of endophytic fungi with their host plants, is an effectively regulatory means to promote the growth and secondary metabolism of medicinal plants. Here, an endophytic fungus Mucor circinelloides DF20 was co-cultivated with the sterile seedlings of S. miltiorrhiza, to clarify the promoting mechanism on tanshinone biosynthesis and accumulation in S. miltiorrhiza root. The assay of promoting-growth activities in vitro showed that DF20 have the ability to produce IAA and siderophores. DF20 could significantly promote the biosynthesis and accumulation of tanshinones in the root of S. miltiorrhiza, especially the content of tanshinone ⅡA, reaching 4.630 ± 0.342 mg/g after 56 days of DF20 treatment, which is 22-fold of the control group. The result also showed that the hyphae of M. circunelloides DF20 mainly colonized in the root tissue interspace of S. miltiorrhiza, and a small amount of hyphae were located inside the cells. The results of florescent real-time quantitative RT-PCR showed that DF20 colonization significantly increase the expression level of some key enzyme genes (DXS, DXR, HMGR, GGPPS) in tanshinone biosynthesis pathway, but the regulatory effect mainly occurred in the early stage of co-culture, while the expression level decreased in different degrees in the later stage. In conclusion, the endophytic fungus M. circunelloides DF20 can form an interaction relationship with its host, then to promote the biosynthesis and accumulation of tanshinones in root by upregulating the key enzyme genes expression levels of the biosynthesis pathway.

Community Composition and Ex Situ Cultivation of Fungi Associated with UNESCO Heritage Monuments in the Bay of Naples

The Bay of Naples, Italy, is renowned for its archaeological heritage. However, this heritage is threatened by the combination of weathering and the biological activity of microorganisms. Fungi are among the major agents of microbial deterioration of cultural heritage since they can cause cracks and lesions in monuments due to the penetrating force of their hyphae. Such biodeterioration may weaken the stone structures and threaten the longevity of these culturally important monuments. To address this, we collected, identified, and maintained in culture filamentous fungi that colonize the external surface of monuments at five important archaeological sites near Naples, namely Cuma, Ercolano, Nola, Oplonti, and Pompei. We isolated a total of 27 fungal taxa, all of which can be cultivated in the laboratory, and form a part of our reference collection. Many of the described fungal taxa we found belong to groups that are involved in stone biodeterioration and can thus be considered as model organisms for in vitro studies. These results emphasize the importance of identifying and cultivating fungal stock cultures for non-invasive studies on biodeterioration. Our newly developed reference collection represents a useful resource that is available to other researchers to rapidly identify potentially hazardous fungi on other monuments.

Mucor rongii sp. nov., a New Cold-Tolerant Species from China

Two strains of a new mucoralean fungus (M1 and R1) were harvested from the moist walls of Sufu workshop in Liaocheng city, Shandong province, China. Internal transcribed spacer (ITS) and the large subunit (LSU) rDNA region D1/D2 domain-based phylogenetic analysis, along with phenotypic characteristics, revealed that the strains belonged to a new genus in the Mucor category. This new category belongs to Mucor flavus complex. However, unlike M. flavus CBS 234.25 (the type species of the complex), the novel species could grow well at 25 °C and not grow at 28 °C. Moreover, the ITS rDNA sequence similarity of the two species was only 96%. Here, we present the new category Mucor rongii sp. nov. Its holotype is HMAS 248,091, the ex-type culture is M1^T (= CICC 41725^T), and the other culture examined was R1 (= CICC 41,726).

Frequency of occurrence, seasonal variation and antifungal susceptibility of opportunistic Mucorales isolated from hospital soils in Iran

BACKGROUND

Mucorales are opportunistic pathogens that can cause life-threatening diseases predominantly in immunocompromised patients.

OBJECTIVES

This study aimed to investigate the frequency, seasonal variation and antifungal susceptibility of pathogenic Mucorales in the soil collected from seven hospitals in Urmia, Iran, between November 2017 and July 2018 in four different seasons.

METHODS

Mucorales isolates obtained from soil were characterised based on conventional and molecular assays. In addition, in vitro antifungal susceptibility was performed using the CLSI M38Ed3 procedure.

RESULTS

Out of 196 tested soil samples, 80 (40.8%) samples were positive for mucoralean fungi. Rhizopus arrhizus var. arrhizus (n = 47) was the most frequent species followed by Mucor circinelloides (n = 21) and Cunninghamella echinulata (n = 6). A seasonal variation in the frequency of Mucorales in soil was detected with a maximum of culture-positive soil samples detected in wet autumn (43.2%) followed by winter (23.4%), summer (19.7%) and spring (13.6%). In vitro antifungal susceptibility testing for 80 environmental isolates exhibited MIC of ≤2 μg/ml for amphotericin B indicating the smallest range of MIC variation among the tested Mucorales (range: 0.125-2 μg/ml). Among the azoles, posaconazole was the most effective antifungals (GM MIC, 0.724 μg/ml).

CONCLUSIONS

We considered associations of species and seasonal frequencies between soil mucoralean fungi and mucormycosis. The effect of opportunistic Mucorales dominating in the soil and prevalent causative agents of mucormycosis in Iran reported in the literatures but more comprehensive studies are needed to confirm this conclusion.

Two New Species in the Family Cunninghamellaceae from China

The species within the family Cunninghamellaceae are widely distributed and produce important metabolites. Morphological studies along with a molecular phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) of ribosomal DNA revealed two new species in this family from soils in China, that is, Absidia ovalispora sp. nov. and Cunninghamella globospora sp. nov. The former is phylogenetically closely related to Absidia koreana, but morphologically differs in sporangiospores, sporangia, sporangiophores, columellae, collars, and rhizoids. The latter is phylogenetically closely related to Cunninghamella intermedia, but morphologically differs in sporangiola and colonies. They were described and illustrated.

Molecular Markers of Antifungal Resistance: Potential Uses in Routine Practice and Future Perspectives

Antifungal susceptibility testing (AST) has come to establish itself as a mandatory routine in clinical practice. At the same time, the mycological diagnosis seems to have headed in the direction of non-culture-based methodologies. The downside of these developments is that the strains that cause these infections are not able to be studied for their sensitivity to antifungals. Therefore, at present, the mycological diagnosis is correctly based on laboratory evidence, but the antifungal treatment is undergoing a growing tendency to revert back to being empirical, as it was in the last century. One of the explored options to circumvent these problems is to couple non-cultured based diagnostics with molecular-based detection of intrinsically resistant organisms and the identification of molecular mechanisms of resistance (secondary resistance). The aim of this work is to review the available molecular tools for antifungal resistance detection, their limitations, and their advantages. A comprehensive description of commercially available and in-house methods is included. In addition, gaps in the development of these molecular technologies are discussed.

Epidemiology of Mucormycosis in India

Mucormycosis is an angioinvasive disease caused by saprophytic fungi of the order Mucorales. The exact incidence of mucormycosis in India is unknown due to the lack of population-based studies. The estimated prevalence of mucormycosis is around 70 times higher in India than that in global data. Diabetes mellitus is the most common risk factor, followed by haematological malignancy and solid-organ transplant. Patients with postpulmonary tuberculosis and chronic kidney disease are at additional risk of developing mucormycosis in this country. Trauma is a risk factor for cutaneous mucormycosis. Isolated renal mucormycosis in an immunocompetent host is a unique entity in India. Though Rhizopus arrhizus is the most common etiological agent of mucormycosis in this country, infections due to Rhizopus microsporus, Rhizopus homothallicus, and Apophysomyces variabilis are rising. Occasionally, Saksenaea erythrospora, Mucor irregularis, and Thamnostylum lucknowense are isolated. Though awareness of the disease has increased among treating physicians, disease-associated morbidity and mortality are still high, as patients seek medical attention late in the disease process and given the low affordability for therapy. In conclusion, the rise in the number of cases, the emergence of new risk factors and causative agents, and the challenges in managing the disease are important concerns with mucormycosis in India.

Tempeh: A semicentennial review on its health benefits, fermentation, safety, processing, sustainability, and affordability

Tempeh is a fermented food made of mainly soybeans and is a nutritious, affordable, and sustainable functional source of protein. Globally, tempeh is a widely accepted fermented product. Although there is a growing body of literature on tempeh, most research has focused on unfermented soybeans, thus the impact of tempeh fermentation on biological properties of soybeans has been largely left scattered. The objective of this review is to summarize the literature of tempeh fermentation over the past 60 years. A search of articles on tempeh published from 1960 to 2020 was performed using the Cochrane Library, Web of Science, EBSCOhost FSTA database, and Google Scholar. References from identified articles were reviewed for additional sources. In total, 321 papers were selected for this review, of which 64 papers were related to the health benefits of tempeh. This review concluded that sufficient evidence exists in the literature supporting tempeh fermentation as a low-cost, health-promoting, and sustainable food processing technology to produce protein-rich foods using various beans, legumes, and grains. This comprehensive review suggests further studies are needed on tempeh fermentation and its impact on human health; research and standardization of nonsoy tempeh; assessment of food safety-improving modification in tempeh production system; and initiatives supporting the sourcing of local ingredients in tempeh production.

Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina

Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.

First occurrence of Backusella gigacellularis (Mucorales, Mucoromycota) in a fragment of an Upland Forest within the semi-arid region of northeastern Brazil

Abstract In a survey mucoralean fungi in the Brejo da Serra do Benedito, a fragment of Upland Forest in the semi-arid region of Pernambuco, Brazil, a specimen of Backusella gigacellularis was isolated. So far, B. gigacellularis (holotype) had only been isolated from soil in the Cerrado domain, in São Paulo state, southeastern Brazil. This is the second report of B. gigacellularis worldwide, and the first record to northeastern Brazil. A detailed description, as well as the illustration of the specimen, are presented.

Dry-aged beef manufactured in Japan: Microbiota identification and their effects on product characteristics

We aimed to determine the mold, yeast, and bacterial distributions in dry-aged beef (DAB) manufactured in Hokkaido, Japan, and to study their effects on meat quality compared to wet-aged beef (WAB). Two rump blocks from Holstein steer were dry- and wet-aged for 35 days at 2.9 °C and 90% RH. The psychrophilic molds Mucor flavus and Helicostylum pulchrum and other fungi (Penicillium sp. and Debaryomyces sp.) appeared on the crust of DAB, while lactic acid bacteria and coliforms were suppressed in the inner part of the meat. The composition of C16:0, C18:0, and C18:1 fatty acids did not differ between DAB and WAB, while more C17:0 fatty acids were detected in DAB. Dry aging suppressed acids and increased the production of various aroma compounds with mushroom-like, nutty, and other pleasant flavors. The meat quality and free amino acid (FAA) contents of DAB and WAB did not differ significantly. In this study, we identified major molds on DAB, which might contribute to an increase in aroma. Keywords: dry-aged beef; Mucor flavus; Helicostylum pulchrum; psychrophilic mold; meat quality; volatile aroma compounds.

One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020)

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.

Rhino-orbital mucormycosis due to Apophysomyces ossiformis in a patient with diabetes mellitus: a case report

Background

The most common aetiological agents of mucormycosis are Rhizopus, Mucor, Apophysomyces and Lichtheimia. Apophysomyces is comparatively rare, as it has been reported in less than 3% of mucormycosis cases. The genus Apophysomyces includes six species, and only A. elegans, A. mexicanus, A. variabilis and A. ossiformis have been reported to cause infections in both immunocompetent and immunocompromised patients.

Case presentation

We present a case of a 46-year-old male patient with bilateral blepharoedema, corneal opacity in the left eye and poorly controlled diabetes mellitus. The patient was subjected to total maxillectomy, exenteration of the left orbit and treatment with liposomal amphotericin B. Direct mycological analysis with KOH 10% revealed hyaline, coenocytic, long and wide hyphae. Apophysomyces ossiformis was identified from maxillary biopsy using 18S-ITS1–5.8S-ITS2-28S rRNA gene amplification and sequencing. The patient requested to be transferred to another hospital to continue treatment, where he died on the ninth day after admittance.

Conclusion

To the best of our knowledge, this is the first case of rhino-orbital mucormycosis due to A. ossiformis with a fatal outcome. This case reveals the need to identify the fungus causing mucormycosis with molecular methods to identify adequate treatment therapies for patients with this infection.

Developments in identifying and managing mucormycosis in hematologic cancer patients

INTRODUCTION

Mucormycoses represent a rare but very aggressive class of mold infections occurring in patients with hematological malignancies (HMs). In the past, patients at high risk of invasive mucomycosis (IM) were those affected by acute myeloid leukemia but over the last ten years the prophylaxis with a very effective mold-active drug, such as posaconazole, has completely modified the epidemiology. In fact, IM is now observed more frequently in patients with lymphoproliferative disorders who do not receive antifungal prophylaxis.

AREAS COVERED

The attention was focused on the epidemiology, diagnosis, prophylaxis and treatment of IM in HMs. Authors excluded pediatric patients considering the different epidemiology and differences in treatment given the limitation of the use of azoles in the pediatric field. A systematic literature review was performed using PubMed database listings between February 2014 and February 2020 using the following MeSH terms: leukemia, hematological malignancies, stem cell transplantation, mucormycosis, molds, prophilaxis, treatment.

EXPERT OPINION

The epidemiology of mucormycosis in HMs is changing in the last years. The availability of drugs more effective than in the past against this infection has reduced the mortality; however, a timely diagnosis remains a relevant problem potentially influencing the outcome of hematologic patients with IM.

First case of fatal Rhizomucor miehei endocarditis in an immunocompromised patient

Rhizomucor miehei is a cause of bovine mycotic abortion and mastitis and has rarely been described in human disease. Here, we report the first isolation of R. miehei from native mitral valve tissue in a fatal case of endocarditis that substantiates its pathogenic potential. Apart from morphological criteria, molecular methods were a cornerstone for definite diagnosis.

Control of an outbreak of post-transplant cutaneous mucormycosis by removing the vehicle: An intervention study of contiguous cohorts

BACKGROUND

An outbreak of post-kidney transplant cutaneous mucormycosis (PK-CM), a severe and even fatal complication in immunocompromised patients, occurred in our institution. The objective of this study was to compare the usual fixation of sterile wound dressings with non-sterile elastic bandages and fixation with sterile bandages processed at our centralized sterile services department with regard to PK-CM prevention.

METHODS

We conducted a before-and-after trial in a private tertiary care hospital. The pre-intervention cohort (n = 16) included all patients who had undergone kidney transplant (KT) during the outbreak (June 2010-April 2011), and the post-intervention cohort (n = 49) included all patients who had undergone KT between May 2011 and October 2013. From May 2011, only bandages sterilized by the centralized sterile services department were used to fix wound dressings of KT patients.

RESULTS

Differences in age (50.2 years vs 51.3 years), sex (43.8% male vs 59.2% female), weight (63.3 kg vs 69.7 kg), hemodialysis vintage (55.6 months vs 47.8 months), and other risk factors were not observed between the pre- and post-intervention cohorts, respectively. PK-CM incidence dropped from 25% in the pre-intervention cohort (4/16) to 0% in the post-intervention cohort (0/49). Relative risk was 0 (P = .003).

CONCLUSIONS

With regard to KT patients and sterile wound dressing fixation with non-sterile bandages versus the use of autoclaved bandages, fixation with autoclaved bandages proved to be effective for cutaneous mucormycosis outbreak control and prevention in our institution.

Occurrence and species diversity of human-pathogenic Mucorales in commercial food-stuffs purchased in Paris area

Mucormycoses are life-threatening fungal diseases that affect a variety of patients including those with diabetes mellitus or hematological malignancies. The responsible agents, the Mucorales, are opportunistic pathogens originating from the environment such as soil or decaying organic matter. The aim of the present study was to assess the prevalence and diversity of human-pathogenic species of Mucorales in commercially available foodstuffs in France. All food samples were purchased from January 2014 to May 2015 in France. A total of 159 dried food samples including spices and herbs (n = 68), herbal tea (n = 19), cereals (n = 19), vegetables (n = 14), and other foodstuffs (n = 39) were analyzed. Each strain of Mucorales was identified phenotypically, and molecular identification was performed by ITS sequencing. From the 28 (17.6%) samples that were culture-positive for Mucorales, 30 isolates were recovered. Among the isolates, 13 were identified as Rhizopus arrhizus var. arrhizus, 10 R. arrhizus var. delemar, two Rhizopus microsporus, one Lichtheimia corymbifera, three Lichtheimia ramosa, and one Syncephalastrum racemosum. Culture-positive samples originated from different countries (Europe, Asia) and brands. The samples most frequently contaminated by Mucorales were spices and herbs (19/68, 27.9%), followed by herbal tea (2/19, 10.5%), cereals (2/19, 10.5%), other food products (5/39, 12.8%). The present study showed that human-pathogenic Mucorales were frequently recovered from commercially available foodstuffs in France with a large diversity of species. The potential danger represented by Mucorales present in food for immunocompromised patients should be further analyzed.

Novel Mucoralean Fungus From a Repugnant Substrate: Mucor merdophylus sp. nov., Isolated From Dog Excrement

The repeated observation of dog dung covered by abundant white cottony mycelium in a private garden in the city of Rio de Janeiro, state of Rio de Janeiro (Brazil) prompted an investigation to clarify the identity of the fungus involved. Three different species of mucoralean fungi (together with some ascomycete asexual morphs) were present. Two were identified as belonging to Mycotypha sp. and Thamnostylum sp., and the third belonged to Mucor sp. This publication deals with the full taxonomic elucidation of the latter. Based on morphological, physiological, and molecular data (ITS and LSU rDNA regions), it was recognized that this Mucor differed from all other species. It produces strongly sympodially circinate branched sporangiophores (some with up to four septa) with numerous swellings resembling abortive sporangia. It also has cylindrical, obovoid, pyriform, or ovoid columellae and its sporangiospores are mostly ellipsoid, although some are subglobose and others are irregular. Based on the evidence of the analyzed datasets, the new species Mucor merdophylus is hereby proposed.

Gongronella eborensis sp. nov., from vineyard soil of Alentejo (Portugal)

This study describes a novel fungal species belonging to the genus Gongronella. During a previous work focusing on metalaxyl degradation by Mucorales strains, two isolates from vineyard soil samples collected in the Alentejo region, south Portugal, were identified as a putative novel species based on combined molecular and MALDI-TOF MS data. This new species is described here using a polyphasic approach that combines morphology, internal transcribed spacer of ribosomal DNA (ITS) and 28S ribosomal DNA (LSU) sequence data analysis and proteomic profiling by MALDI-TOF MS. Phenotypic and molecular data enabled this novel species to be clearly distinguished from other Gongronella species with results of combined ITS+LSU analysis showing that the Gongronella species is related to Gongronella butleri and Gongronella brasiliensis. Therefore, from the results of morphological and molecular analyses, isolates MUM 10.262 and MUM 10.263 seem to represent a new Gongronella species and the name Gongronella eborensis sp. nov. is proposed, with the ex-type strain MUM 10.262 (=CCMI 1100=CBS 128763).

Metatranscriptomic Profiling Reveals the Effect of Breed on Active Rumen Eukaryotic Composition in Beef Cattle With Varied Feed Efficiency

Exploring the compositional characteristics of rumen eukaryotic community can expand our understanding of their role in rumen function and feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen eukaryotic community (protozoa and fungi) in beef cattle (n = 48) of three breeds [Angus (AN), Charolais (CH), and Kinsella Composite (KC)] and with divergent residual feed intake (RFI). The composition of active rumen eukaryotic microbiota was evaluated based on enriched 18S rRNAs from the metatranscriptomic datasets. At the phylum level, a total of four protozoal taxa (Ciliophora, Parabasalia, unclassified SAR, and unclassified Alveolata), six fungal taxa (Neocallimastigomycota, Basidiomycota, unclassified Fungi, Mucoromycota, Ascomycota, and Chytridiomycota), and one sister group of kingdom Fungi (unclassified Opisthokonta) were detected with relative abundances higher than 0.01% and in at least 50% of animals within each breed. Among these, Ciliophora, Parabasalia, unclassified Opisthokonta, and Neocallimastigomycota were the top four active eukaryotic phyla. At the genus level, a total of 8 ciliated protozoa, 5 flagellated protozoa, 5 anaerobic fungi, and 10 aerobic fungi taxa were detected, with unclassified Trichostomatia, Tetratrichomonas, unclassified Neocallimastigaceae, and Pleurotus being the most predominant taxa of ciliated protozoa, flagellated protozoa, anaerobic fungi, and aerobic fungi, respectively. Differential abundance analysis revealed that breed had a significant effect on the phylogenetic lineages of rumen eukaryotes, and seven fungal taxa were more abundant (linear discriminant analysis score > 2 with P < 0.05) in the rumen of KC steers than in the rumen of AN and CH steers. Although principal coordinate analysis (PCoA) revealed that the ruminal active eukaryotic profiles were not distinguishable between high- and low-RFI groups, the diversity indices, including Faith’s phylogenetic diversity (PD), observed operational taxonomic units (OTUs), and Shannon index of rumen eukaryotes were higher in low-RFI steers than those in high-RFI steers. Meanwhile, the abundance of genus Entodinium and the kingdom Fungi was higher in low-RFI steers than that in high-RFI steers. This information on active rumen eukaryotic microbiota and identified differential abundance of taxa between high- and low-RFI animals suggests the possibility of improving feed efficiency through altering rumen eukaryotic microbiota.

Comparative genomics applied to Mucor species with different lifestyles

BACKGROUND

Despite a growing number of investigations on early diverging fungi, the corresponding lineages have not been as extensively characterized as Ascomycota or Basidiomycota ones. The Mucor genus, pertaining to one of these lineages is not an exception. To this date, a restricted number of Mucor annotated genomes is publicly available and mainly correspond to the reference species, Mucor circinelloides, and to medically relevant species. However, the Mucor genus is composed of a large number of ubiquitous species as well as few species that have been reported to specifically occur in certain habitats. The present study aimed to expand the range of Mucor genomes available and identify potential genomic imprints of adaptation to different environments and lifestyles in the Mucor genus.

RESULTS

In this study, we report four newly sequenced genomes of Mucor isolates collected from non-clinical environments pertaining to species with contrasted lifestyles, namely Mucor fuscus and Mucor lanceolatus, two species used in cheese production (during ripening), Mucor racemosus, a recurrent cheese spoiler sometimes described as an opportunistic animal and human pathogen, and Mucor endophyticus, a plant endophyte. Comparison of these new genomes with those previously available for six Mucor and two Rhizopus (formerly identified as M. racemosus) isolates allowed global structural and functional description such as their TE content, core and species-specific genes and specialized genes. We proposed gene candidates involved in iron metabolism; some of these genes being known to be involved in pathogenicity; and described patterns such as a reduced number of CAZymes in the species used for cheese ripening as well as in the endophytic isolate that might be related to adaptation to different environments and lifestyles within the Mucor genus.

CONCLUSIONS

This study extended the descriptive data set for Mucor genomes, pointed out the complexity of obtaining a robust phylogeny even with multiple genes families and allowed identifying contrasting potentially lifestyle-associated gene repertoires. The obtained data will allow investigating further the link between genetic and its biological data, especially in terms of adaptation to a given habitat.

Microsatellite analysis of the population structure in Rhizopus arrhizus

OBJECTIVES

Rhizopus arrhizus is recognized as an emergent agent of superficial and invasive mucormycosis. Despite an increasing number of these infections, the molecular epidemiology of Rhizopus species has not been well studied.

MATERIALS AND METHODS

In this study, 43 R. arrhizus strains (25 environmental and 18 clinical isolates) were genotyped using six novel panels of microsatellite markers.

RESULTS

Upon the analysis of 43 isolates, 4-8 distinct alleles were detected for each marker. The discriminatory power for the individual markers ranged from 0·522 to 0·830. The combination of all six markers yielded 33 different haplotypes with a high degree of discrimination (0·989 D value). A four-marker combination were selected as the most parsimonious panel achieving D > 0·95. One clinical isolate and one environmental isolate shared the same genotype suggesting the possible nosocomial outbreak of mucormycosis in hospitalized patients. We have noted that the strains isolated from cutaneous mucormycosis were different from the strains isolated from rhino-orbito-cerebral mucormycosis. Then, the hypothesis of particular tropism of infectious strains for a given site is not excluded. The standardized indices of association IA and rBarD were significantly different from zero (P < 0·01), suggesting a prevailing clonal reproduction. The environmental population was significantly differentiated from clinical populations (Fst = 0·2249).

CONCLUSIONS

Microsatellite typing method described in our study showed an excellent degree of discriminatory power. It is a promising tool for illuminating the molecular epidemiology of R. arrhizus species, including strain relatedness and transmission pathways.

Fungal keratitis: Pathogenesis, diagnosis and prevention

As a kind of serious, potentially sight-threatening corneal infections with poor prognosis, fungal keratitis can bring a heavy economic burden to patients and seriously affect the quality of life, especially those in developing countries where fungal keratitis is more prevalent. Typical clinical features include immune rings, satellite lesions, pseudopods, hypha moss, hypopyon and endothelial plaques. The ideal therapeutic effects could not be achieved by current treatments for many reasons. Therefore, under the current status, understanding the pathogenesis, early diagnosis and prevention strategies might be of great importance. Here, in this review, we discuss the recent progresses that may advance our understanding of pathogenesis, early diagnosis and prevention of fungal keratitis.

Isolation and Characterization of Four Unrecorded Mucor Species in Korea

During an investigation of fungi of the order Mucorales from freshwater and sediment samples in Korea, we isolated six strains, NNIBRFG6649, NNIBRFG6255, NNIBRFG1498, CNUFC-YJ13, CNUFC-YR7, and NNIBRFG2739. The morphology and phylogeny of these strains were analyzed. Based on the morphological characteristics and molecular data from internal transcribed spacer (ITS) region, the isolates NNIBRFG6649 and NNIBRFG6255 were identified as Mucor abundans, and M. aligarensis, respectively. The isolates NNIBRFG1498 and CNUFC-YJ13 were identified as M. moelleri, whereas the isolates CNUFC-YR7 and NNIBRFG2739 were identified as M. heterogamus. To the best of our knowledge, M. abundans, M. aligarensis, M. moelleri, and M. heterogamus have not yet been reported in Korea.

Outbreaks of Mucorales and the Species Involved

The order Mucorales is an ancient group of fungi classified in the subphylum Mucoromycotina. Mucorales are mainly fast-growing saprotrophs that belong to the first colonizers of diverse organic materials and represent a permanent part of the human environment. Several species are able to cause human infections (mucormycoses) predominantly in patients with impaired immune system, diabetes, or deep trauma. In this review, we compiled 32 reports on community- and hospital-acquired outbreaks caused by Mucorales. The most common source of mucoralean outbreaks was contaminated medical devices that are responsible for 40.7% of the outbreaks followed by contaminated air (31.3%), traumatic inoculation of soil or foreign bodies (9.4%), and the contact (6.2%) or the ingestion (6.2%) of contaminated plant material. The most prevalent species were Rhizopus arrhizus and R. microsporus causing 57% of the outbreaks. The genus Rhizomucor was dominating in outbreaks related to contaminated air while outbreaks of Lichtheimia species and Mucor circinelloides were transmitted by direct contact. Outbreaks with the involvement of several species are reported. Subtyping of strains revealed clonality in two outbreaks and no close relation in two other outbreaks. Based on the existing data, outbreaks of Mucorales can be caused by heterogeneous sources consisting of different strains or different species. Person-to-person transmission cannot be excluded because Mucorales can sporulate on wounds. For a better understanding and prevention of outbreaks, we need to increase our knowledge on the physiology, ecology, and population structure of outbreak causing species and more subtyping data.

Updates on the Taxonomy of Mucorales with an Emphasis on Clinically Important Taxa

Fungi of the order Mucorales colonize all kinds of wet, organic materials and represent a permanent part of the human environment. They are economically important as fermenting agents of soybean products and producers of enzymes, but also as plant parasites and spoilage organisms. Several taxa cause life-threatening infections, predominantly in patients with impaired immunity. The order Mucorales has now been assigned to the phylum Mucoromycota and is comprised of 261 species in 55 genera. Of these accepted species, 38 have been reported to cause infections in humans, as a clinical entity known as mucormycosis. Due to molecular phylogenetic studies, the taxonomy of the order has changed widely during the last years. Characteristics such as homothallism, the shape of the suspensors, or the formation of sporangiola are shown to be not taxonomically relevant. Several genera including Absidia, Backusella, Circinella, Mucor, and Rhizomucor have been amended and their revisions are summarized in this review. Medically important species that have been affected by recent changes include Lichtheimia corymbifera, Mucor circinelloides, and Rhizopus microsporus. The species concept of Rhizopus arrhizus (syn. R. oryzae) is still a matter of debate. Currently, species identification of the Mucorales is best performed by sequencing of the internal transcribed spacer (ITS) region. Ecologically, the Mucorales represent a diverse group but for the majority of taxa, the ecological role and the geographic distribution remain unknown. Understanding the biology of these opportunistic fungal pathogens is a prerequisite for the prevention of infections, and, consequently, studies on the ecology of the Mucorales are urgently needed.

A new species concept for the clinically relevant Mucor circinelloides complex

Mucor species are common soil fungi but also known as agents of human infections (mucormycosis) and used in food production and biotechnology. Mucor circinelloides is the Mucor species that is most frequently isolated from clinical sources. The taxonomy of Mucor circinelloides and its close relatives (Mucor circinelloides complex – MCC) is still based on morphology and mating behaviour. The aim of the present study was a revised taxonomy of the MCC using a polyphasic approach. Using a set of 100 strains molecular phylogenetic analysis of five markers (ITS, rpb1, tsr1, mcm7, and cfs, introduced here) were performed, combined with phenotypic studies, mating tests and the determination of the maximum growth temperatures. The multi-locus analyses revealed 16 phylogenetic species of which 14 showed distinct phenotypical traits and were recognised as discrete species. Five of these species are introduced as novel taxa: M. amethystinus sp. nov., M. atramentarius sp. nov., M. variicolumellatus sp. nov., M. pseudocircinelloides sp. nov., and M. pseudolusitanicus sp. nov. The former formae of M. circinelloides represent one or two separate species. In the MCC, the simple presence of well-shaped zygospores only indicates a close relation of both strains, but not necessarily conspecificity. Seven species of the MCC have been implemented in human infection: M. circinelloides, M. griseocyanus, M. janssenii, M. lusitanicus, M. ramosissimus, M. variicolumellatus, and M. velutinosus.

Carbon assimilation profiles of mucoralean fungi show their metabolic versatility

Most mucoralean fungi are common soil saprotrophs and were probably among the first land colonisers. Although Mucoromycotina representatives grow well on simple sugar media and are thought to be unable to assimilate more complex organic compounds, they are often isolated from plant substrates. The main goal of the study was to explore the effects of isolation origin and phylogenetic placement on the carbon assimilation capacities of a large group of saprotrophic Mucoromycotina representatives (i.e. Umbelopsidales and Mucorales). Fifty two strains representing different Mucoromycotina families and isolated from different substrates were tested for their capacity to grow on 99 different carbon sources using the Biolog phenotypic microarray system and agar plates containing selected biopolymers (i.e. cellulose, xylan, pectin, and starch) as a sole carbon source. Although our results did not reveal a correlation between phylogenetic distance and carbon assimilation capacities, we observed 20 significant differences in growth capacity on specific carbon sources between representatives of different families. Our results also suggest that isolation origin cannot be considered as a main predictor of the carbon assimilation capacities of a particular strain. We conclude that saprotrophic Mucoromycotina representatives are, contrary to common belief, metabolically versatile and able to use a wide variety of carbon sources.

A Revised Species Concept for Opportunistic Mucor Species Reveals Species-Specific Antifungal Susceptibility Profiles

Recently, the species concept of opportunistic Mucor circinelloides and its relatives has been revised, resulting in the recognition of its classical formae as independent species and the description of new species. In this study, we used isolates of all clinically relevant Mucor species and performed susceptibility testing using the EUCAST reference method to identify potential species-specific susceptibility patterns. In vitro susceptibility profiles of 101 mucoralean strains belonging to the genus Mucor (72), the closely related species Cokeromyces recurvatus (3), Rhizopus (12), Lichtheimia (10), and Rhizomucor (4) to six antifungals (amphotericin B, natamycin, terbinafine, isavuconazole, itraconazole, and posaconazole) were determined. The most active drug for all Mucorales was amphotericin B. Antifungal susceptibility profiles of pathogenic Mucor species were specific for isavuconazole, itraconazole, and posaconazole. The species formerly united in M. circinelloides showed clear differences in their antifungal susceptibilities. Cokeromyces recurvatus, Mucor ardhlaengiktus, Mucor lusitanicus (M. circinelloides f. lusitanicus), and Mucor ramosissimus exhibited high MICs to all azoles tested. Mucor indicus presented high MICs for isavuconazole and posaconazole, and Mucor amphibiorum and Mucor irregularis showed high MICs for isavuconazole. MIC values of Mucor spp. for posaconazole, isavuconazole, and itraconazole were high compared to those for Rhizopus and the Lichtheimiaceae (Lichtheimia and Rhizomucor). Molecular identification combined with in vitro susceptibility testing is recommended for Mucor species, especially if azoles are applied in treatment.

Diversity of thermophilic and thermotolerant fungi in corn grain

Corn bins in the midwestern United States can reach temperatures up to 52 C. High temperatures combined with sufficient moisture and humidity in bins provide the perfect environment to promote the growth of thermophilic and thermotolerant fungi. In this article, we characterize for the first time thermophilic and thermotolerant fungi in corn grain bins using culture-based methods and pyrosequencing techniques. Corn samples were collected from local farms in western Illinois. Samples were plated and incubated at 50 C using a variety of approaches. Of several hundred kernels examined, more than 90% showed colonization. Species identified using culture methods included Thermomyces lanuginosus, Thermomyces dupontii, Aspergillus fumigatus, Thermoascus crustaceus, and Rhizomucor pusillus. Pyrosequencing was also performed directly on corn grain using fungal-specific primers to determine whether thermophilic fungi could be detected using this technique. Sequences were dominated by pathogenic fungi, and thermophiles were represented by less than 2% of the sequences despite being isolated from 90% of the grain samples using culturing techniques. The high abundance of previously undocumented viable fungi in corn could have negative implications for grain quality and pose a potential risk for workers and consumers of corn-derived products in the food industry. Members of the Sordariales were absent among thermophile isolates and were not represented in nuc rDNA internal transcribed spacer (ITS) sequences. This is in striking contrast with results obtained with other substrates such as litter, dung, and soils, where mesophilic and thermophilic members of the Sordariaceae and Chaetomiaceae are common. This absence appears to reflect an important difference between the ecology of Sordariales and other orders within the Ascomycota in terms of their ability to compete in microhabitats rich in sugars and living tissues.

Endophytic fungi from the branches of Camellia taliensis (W. W. Smith) Melchior, a widely distributed wild tea plant

Camellia taliensis (W. W. Smith) Melchior is a wild tea plant endemic from the west and southwest of Yunnan province of China to the north of Myanmar and is used commonly to produce tea by the local people of its growing areas. Its chemical constituents are closely related to those of C. sinensis var. assamica, a widely cultivated tea plant. In this study, the α diversity and phylogeny of endophytic fungi in the branches of C. taliensis were explored for the first time. A total of 160 fungal strains were obtained and grouped into 42 species from 29 genera, which were identified based on rDNA internal transcribed spacer sequence analysis. Diversity analysis showed that the endophytic fungal community of the branches of C. taliensis had high species richness S (42), Margalef index D' (8.0785), Shannon-Wiener index H' (2.8494), Simpson diversity index D_S (0.8891), PIE index (0.8947) and evenness Pielou index J (0.7623) but a low dominant index λ (0.1109). By contrast, that in the branches of C. taliensis had abundant species and high species evenness. Diaporthe tectonigena, Acrocalymma sp. and Colletotrichum magnisporum were the dominant endophytic fungi. The phylogenetic tree was established by maximum parsimony analysis, and the 11 orders observed for endophytic fungi belonging to Ascomycota and Basidiomycota were grouped into 4 classes.

Microbiomes in an acidic rock-water cave system

Belowground ecosystems are accessible by mining, where a specific microbial community can be discovered. The biodiversity of a former alum mine rich in carbon, but with a low pH of 2.6-3.7, was evaluated by DNA- and cultivation-dependent methods using samples of the black slate rock material, secondary mineralization phases and seepage water. Pyrite oxidation within the low-grade metamorphic Silurian black slate established high concentrations of Fe and $\rm{SO}_4^{2-}$ forming the extreme conditions visible with acidophilic and Fe-oxidizing microorganisms. In addition, an unexpected predominance of fungi in this C-rich and acidic cave ecosystem, including high numbers of Mucoromycota and Mortierellomycota, was detected. Therefore, fungal cultures were obtained, mainly from the secondary mineral phases that are iron phosphates. Hence, the fungi might well have been involved in phosphate mobilization there. The rock material itself is rich in organic carbon that can be used by oxidase activity. The cultivation setup mimicked the cave conditions (low temperature, low pH, oxic conditions), with one oligotrophic and one medium rich in nutrients that allowed for isolation of different fungal (and eutrophic bacterial) groups. The acidic conditions prevented the occurrence of many basidiomycetes, while the isolated fungi could survive these adverse conditions.

In Vitro Activity of Combinations of Zinc Chelators with Amphotericin B and Posaconazole against Six Mucorales Species

Mucormycosis is an emerging disease with high mortality rates. Few antifungal drugs are active against Mucorales. Considering the low efficacy of monotherapy, combination-therapy strategies have been described. It is known that fungi are susceptible to zinc deprivation, so we tested the in vitro effect of the zinc chelators clioquinol, phenanthroline, and N,N,N',N'-tetrakis(2-pyridylmethyl)ethane-1,2-diamine combined with amphotericin B or posaconazole against 25 strains of Mucorales. Clioquinol-posaconazole was the most active combination, although results were strain dependent.

Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity

Thermophilic fungi can represent a rich source of industrially relevant enzymes. Here, 105 fungal strains capable of growing at 50 °C and pH 2.0 were isolated from compost and decaying plant matter. Maximum growth temperatures of the strains were in the range 50 °C to 60 °C. Sequencing of the internal transcribed spacer (ITS) regions indicated that 78 fungi belonged to 12 species of Ascomycota and 3 species of Zygomycota, while no fungus of Basidiomycota was detected. The remaining 27 strains could not be reliably assigned to any known species. Phylogenetically, they belonged to the genus Thielavia, but they represented 23 highly divergent genetic groups different from each other and from the closest known species by 12 to 152 nucleotides in the ITS region. Fungal secretomes of all 105 strains produced during growth on untreated rice straw were studied for lignocellulolytic activity at different pH and temperatures. The endoglucanase and xylanase activities differed substantially between the different species and strains, but in general, the enzymes produced by the novel Thielavia spp. strains exhibited both higher thermal stability and tolerance to acidic conditions. The study highlights the vast potential of an untapped diversity of thermophilic fungi in the tropics.

Diversity of cytosine methylation across the fungal tree of life

The generation of thousands of fungal genomes is leading to a better understanding of genes and genomic organization within the kingdom. However, the epigenome, which includes DNA and chromatin modifications, remains poorly investigated in fungi. Large comparative studies in animals and plants have deepened our understanding of epigenomic variation, particularly of the modified base 5-methylcytosine (5mC), but taxonomic sampling of disparate groups is needed to develop unifying explanations for 5mC variation. Here we utilize the largest phylogenetic resolution of 5mC methyltransferases (5mC MTases) and genome evolution to better understand levels and patterns of 5mC across fungi. We show that extant 5mC MTase genotypes are descendent from ancestral maintenance and de novo genotypes, whereas the 5mC MTases DIM-2 and RID are more recently derived, and that 5mC levels are correlated with 5mC MTase genotype and transposon content. Our survey also revealed that fungi lack canonical gene body methylation, which distinguishes fungal epigenomes from certain insect and plant species. However, some fungal species possess independently derived clusters of contiguous 5mC encompassing many genes. In some cases, DNA repair pathways and the N6-methyladenine (6mA) DNA modification negatively coevolved with 5mC pathways, which additionally contributed to interspecific epigenomic variation across fungi.

In Vitro and In Vivo Evaluation of Voriconazole-Containing Antifungal Combinations against Mucorales Using a Galleria mellonella Model of Mucormycosis

Mucorales are resistant to most antifungals. Mucormycosis associated mortality is unacceptable and new treatment approaches are needed. The objectives of this work were (i) to evaluate the nature and intensity of the in vitro effect of three drugs combinations which included voriconazole (plus amphotericin B, posaconazole and caspofungin) against 25 strains of six different Mucorales species; (ii) to evaluate a Galleria mellonella mucormycosis model; and (iii) to establish if any in vitro⁻in vivo correlation exists. As expected, amphotericin B and posaconazole were the most active drugs when tested alone. However, species-specific differences were found. The ΣFICs varied according to the used combination. Only five strains showed synergism when voriconazole was combined with posaconazole and three strains when combined with amphotericin B. Microscopic hyphae alteration were observed for some isolates when confronted against drugs combinations. Using a Galleria mellonella mucormycosis model, better survival was seen in voriconazole plus amphotericin B and plus caspofungin combined treatments when compared with AMB alone for R. microsporus. These survival improvements were obtained using a 32-fold lower amphotericin B doses when combined with VRC than when treated with the polyene alone. These lower antifungal doses emulate the antifungal concentrations where the microscopic hyphae alterations were seen.

Fulminant mucormycosis after a traffic accident: a case report

Mucormycosis is a rare fungal infection in immunocompetent patients, whereas in immunocompromised, it may be systemic and disseminated infection associated with high mortality. Mucormycosis is one of the most rapidly progressing and fulminant forms of fungal infections; Mucor circinelloides is rarely isolated species, also from immunocompromised patients. The reported case of mucormycosis after a traffic accident indicates that it may be the result of a contamination of wound by M. circinelloides coming from the environment. The fungal strain was identified by phenotypic methods and confirmed by molecular methods. Etest method was used for susceptibility testing of the fungal strain. No mycotoxins were detected in the analyzed sample. The infection was successfully treated with amphotericin B, but amputation of the lower limb was necessary.