Microfungi in cultivated fields in Eskişehir provience (Turkey)

New plectosphaerellaceous species from Dutch garden soil

During 2017, the Westerdijk Fungal Biodiversity Institute (WI) and the Utrecht University Museum launched a Citizen Science project. Dutch school children collected soil samples from gardens at different localities in the Netherlands, and submitted them to the WI where they were analysed in order to find new fungal species. Around 3000 fungal isolates, including filamentous fungi and yeasts, were cultured, preserved and submitted for DNA sequencing. Through analysis of the ITS and LSU sequences from the obtained isolates, several plectosphaerellaceous fungi were identified for further study. Based on morphological characters and the combined analysis of the ITS and TEF1-α sequences, some isolates were found to represent new species in the genera Phialoparvum, i.e. Ph. maaspleinense and Ph. rietveltiae, and Plectosphaerella, i.e. Pl. hanneae and Pl. verschoorii, which are described and illustrated here.

The Good, the Bad, and the Ugly: Tales of Mold-Ripened Cheese

The history of cheese manufacture is a "natural history" in which animals, microorganisms, and the environment interact to yield human food. Part of the fascination with cheese, both scientifically and culturally, stems from its ability to assume amazingly diverse flavors as a result of seemingly small details in preparation. In this review, we trace the roots of cheesemaking and its development by a variety of human cultures over centuries. Traditional cheesemakers observed empirically that certain environments and processes produced the best cheeses, unwittingly selecting for microorganisms with the best biochemical properties for developing desirable aromas and textures. The focus of this review is on the role of fungi in cheese ripening, with a particular emphasis on the yeast-like fungus Geotrichum candidum. Conditions that encourage the growth of problematic fungi such as Mucor and Scopulariopsis as well as Arachnida (cheese mites), and how such contaminants might be avoided, are discussed. Bethlehem cheese, a pressed, uncooked, semihard, Saint-Nectaire-type cheese manufactured in the United Sates without commercial strains of bacteria or fungi, was used as a model for the study of stable microbial succession during ripening in a natural environment. The appearance of fungi during a 60-day ripening period was documented using light and scanning electron microscopy, and it was shown to be remarkably reproducible and parallel to the course of ripening of authentic Saint-Nectaire cheese in the Auvergne region of France. Geotrichum candidum, Mucor, and Trichothecium roseum predominate the microbiotas of both cheese types. Geotrichum in particular was shown to have high diversity in different traditional cheese ripening environments, suggesting that traditional manufacturing techniques selected for particular fungi. This and other studies suggest that strain diversity arises in relation to the lore and history of the regions from which these types of cheeses arose.

Combat-Related Invasive Fungal Wound Infections

Combat-related invasive fungal (mold) wound infections (IFIs) have emerged as an important and morbid complication following explosive blast injuries among military personnel. Similar to trauma-associated IFI cases among civilian populations, as in agricultural accidents and natural disasters, these infections occur in the setting of penetrating wounds contaminated by environmental debris. Specific risk factors for combat-related IFI include dismounted (patrolling on foot) blast injuries occurring mostly in southern Afghanistan, resulting in above knee amputations requiring resuscitation with large-volume blood transfusions. Diagnosis of IFI is based upon early identification of a recurrently necrotic wound following serial debridement and tissue-based histopathology examination with special stains to detect invasive disease. Fungal culture of affected tissue also provides supportive information. Aggressive surgical debridement of affected tissue is the primary therapy. Empiric antifungal therapy should be considered when there is a strong suspicion for IFI. Both liposomal amphotericin B and voriconazole should be considered initially for treatment since many of the cases involve not only Mucorales species but also Aspergillus or Fusarium spp., with narrowing of regimen based upon clinical mycology findings.

Effects of dry olive residue transformed by Coriolopsis floccosa (Polyporaceae) on the distribution and dynamic of a culturable fungal soil community

Dry olive residue (DOR) is an abundant waste product resulting from a two-phase olive oil extraction system. Due to its high organic and mineral content, this material has been proposed as an organic soil amendment; however, it presents phytotoxic and microtoxic properties. Thus, a pretreatment is necessary before its application to soil. Among the strategies for the bioremediation of DOR is treatment with ligninolytic fungi, e.g. Coriolopsis floccosa. This work aimed to assess the diversity of culturable fungi in a soil of the southeast Iberian Peninsula and to evaluate the short-term impact of untransformed and C. floccosa-transformed DOR on soil mycobiota. A total of 1,733 strains were isolated by the particle filtration method and were grouped among 109 different species using morphological and molecular methods. The majority of isolates were ascomycetes and were concentrated among three orders: Hypocreales, Eurotiales and Capnodiales. The soil amendment with untransformed DOR was associated with a depression in fungal diversity at 30 days and changes in the proportions of the major species. However, when C. floccosa-transformed DOR was applied to the soil, changes in fungal diversity were less evident, and species composition was similar to unamended soil.

Genetic diversity and mating types of Fusarium culmorum and Fusarium graminearum originating from different agro-ecological regions in Turkey

Fusarium culmorum and F. graminearum are the major pathogens for dryland root/foot-rot and head-blight diseases in economically important grain crops. This study was aimed at the molecular characterization of Fusarium spp. isolates, which have been collected from cereal fields in three agro-ecological regions in Turkey. Genetic diversity has been analyzed by generating RFLP markers from the intergenic spacer (IGS) region of ribosomal RNA. The selection of restriction enzymes for IGS-RFLP studies has been found critical to maximize polymorphic markers. Only 3 of 14 restriction endonucleases were useful in differentiating Fusarium spp. isolates. PstI was the most efficient enzyme to produce a maximum of nine DNA markers in one individual and total 22 polymorphic representative banding patterns. Polymorphism based on IGS-RFLP was high and average 88% in both species. There was no association between IGS diversity and geographic locations from which the samples were taken. Both MAT-1 and MAT-2 sequences were amplified in F. graminearum similarly to previous reports. Most of the F. culmorum isolates carried either MAT-1 or MAT-2 sequences, and differently two isolates carried both sequences. Mating type determination was helpful to distinguish F. pseudograminearum from F. graminearum, which cannot be discriminated by SCAR markers or morphological assessment. High genetic diversity by IGS-RFLP markers in F. culmorum was discussed in relation to its fitness as the most common pathogen in dryland root rot complex (DLRRC).

Biodiversity of the genus Fusarium in saline soil habitats

Fusarium species assemblage and diversity were investigated in eight different contrasting extreme saline soil habitats of the hot arid desert environment of Bahrain. Saline habitats are located towards the central-southern part of Bahrain and featured by high electrical conductivity, slightly alkaline sandy soil, poor in nutrient sources and water holding capacity and mainly dominated by a salt-tolerant flora. Quantification of data for the recovery of Fusarium species was based on morphological characters and counts by a series of ten fold dilutions plate method and direct soil plating, using two selective media supplemented with different NaCl concentrations. A total of 68 isolates, fluctuated between 1 and 23 per soil sample, were recovered among all habitats mostly at 0 and 5% NaCl concentrations, while no recovery was achieved at 20 and 25%. Grouping of these isolates has resulted in only five species (F. solani, F. oxysporum, F. chlamydosporum, F. equiseti and F. compactum), all of which were previously reported from the arid terrestrial habitats of Bahrain. F. solani was the most predominant species, based on relative density, frequency of occurrence and dominance values, followed by F. oxysporum, a finding consistent with other similar arid Sahara ecosystems. Evaluation of data, supported by analysis of diversity indices and community coefficients, revealed that desert mountain habitat followed by burial mounds habitat were highly homogeneous coupled with maximum species richness, diversity indices and evenness, whereas soil habitats like cliffs, coastal and Al-Lowzy pit were the poorest. Moreover, in vitro tests showed that among other fusaria, F. solani exhibited the highest tolerance to increase NaCl concentrations (25%) and temperature (28.3 mm linear growth at 35 degrees C). At 10% NaCl concentrations, significant reduction in linear growth extensions suppressed all species accompanied by massive thick-walled, drought-resistant chlamydospores formation, indicating that species are mainly thermo-osmotolerant. Fusarium species recoveries were negatively significantly correlated (p < 0.05), with soil edaphic factors including salinity (r = -0.849) and soil moisture (r = -0.711). It is thus, proposed that inter and intra specific variation in the Fusarium species community, in particular soil niche, is an outcome of the influence of bioclimatic, multi-soil-edaphic and biotic factors.