keratitis is a destructive eye infection that is difficult to treat and results in poor outcome. In tropical and subtropical areas, the infection is relatively common and associated with trauma or chronic eye diseases. However, in recent years, an increased incidence has been reported in temperate climate regions. At the German National Reference Center, we have observed a steady increase in case numbers since 2014. Here, we present the first German case series of eye infections with species. We identified isolates from the eye or eye-related material from 22 patients in 2014 and 2015. Thirteen isolates belonged to the species complex (FSSC), 6 isolates belonged to the species complex (FOSC), and three isolates belonged to the species complex (FFSC). FSSC was isolated in 13 of 15 (85%) definite infections and FOSC in 3 of 4 (75%) definite contaminations. Furthermore, diagnosis from contact lens swabs or a culture of contact lens solution turned out to be highly unreliable. FSSC isolates differed from FOSC and FFSC by a distinctly higher MIC for terbinafine. Outcome was often adverse, with 10 patients requiring keratoplasty or enucleation. The use of natamycin as the most effective agent against keratitis caused by filamentous fungi was rare in Germany, possibly due to restricted availability. Keratitis caused by spp. (usually FSSC) appears to be a relevant clinical problem in Germany, with the use of contact lenses as the predominant risk factor. Its outcome is often adverse.

Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1–4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparision to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.

SummaryBasidiobolus ranarum (Entomophthoromycotina) very rarely affects the gastrointestinal (GI) tract. To date, reported paediatric GI basidiobolomycosis cases are 27 worldwide; 19 from Saudi Arabia and 8 from other parts of the world. Often these cases present a diagnostic dilemma, are prone to misdiagnosis and lack of disease confirmation by proper molecular methodologies. The fungal mass removed by surgery is usually sent for conciliar histopathology, isolation by fungal cultures and final molecular testing for basidiobolomycosis. The incidence of basidiobolomycoses, their predisposing factors and the molecular diagnosis of the fungus causing the disease in combination with a phylogenetic framework are reviewed.

Anaerobic fungi are potent fibre degrading microbes in the equine hindgut, yet our understanding of their diversity and community structure is limited to date. In this preliminary work, using a clone library approach we studied the diversity of anaerobic fungi along six segments of the horse hindgut: caecum, right ventral colon (RVC), left ventral colon (LVC), left dorsal colon (LDC), right dorsal colon (RDC) and rectum. Of the 647 ITS1 clones, 61.7% were assigned to genus level groups that are so far without any cultured representatives, and 38.0% were assigned to the cultivated genera Neocallimastix (35.1%), Orpinomyces (2.3%), and Anaeromyces (0.6%). AL1 dominated the group of uncultured anaerobic fungi, particularly in the RVC (88%) and LDC (97%). Sequences from the LSU clone library analysis of the LDC, however, split into two distinct phylogenetic clusters with low sequence identity to Caecomyces sp. (94-96%) and Liebetanzomyces sp. (92%) respectively. Sequences belonging to cultured Neocallimastix spp. dominated in LVC (81%) and rectum (75.5%). Quantification of anaerobic fungi showed significantly higher concentrations in RVC and RDC compared to other segments, which influenced the interpretation of the changes in anaerobic fungal diveristy along the horse hindgut. These preliminary findings require further investigation.

Mycology, the study of fungi, originated as a sub discipline of botany and was a descriptive discipline, largely neglected as an experimental science until the early years of this century. A seminal paper by Blakeslee in 1904 provided evidence for self-incompatibility, termed "heterothallism," and stimulated interest in studies related to the control of sexual reproduction in fungi by mating-type specificities. Soon to follow was the demonstration that sexually reproducing fungi exhibit Mendelian inheritance and that it was possible to conduct formal genetic analysis with fungi. The names Burgeff, Kniep and Lindegren are all associated with this early period of fungal genetics research.These studies and the discovery of penicillin by Fleming, who shared a Nobel Prize in 1945, provided further impetus for experimental research with fungi. Thus, began a period of interest in mutation induction and analysis of mutants for biochemical traits. Such fundamental research, conducted largely with Neurospora crassa, led to the one gene:one enzyme hypothesis and to a second Nobel Prize for fungal research awarded to Beadle and Tatum in 1958. Fundamental research in biochemical genetics was extended to other fungi, especially to Saccharomyces cerevisiae, and by the mid-1960s fungal systems were much favored for studies in eukaryotic molecular biology and were soon able to compete with bacterial systems in the molecular arena.The experimental achievements in research on the genetics and molecular biology of fungi have benefited more generally studies in the related fields of fungal biochemistry, plant pathology, medical mycology, and systematics. Today, there is much interest in the genetic manipulation of fungi for applied research. This current interest in biotechnical genetics has been augmented by the development of DNA-mediated transformation systems in fungi and by an understanding of gene expression and regulation at the molecular level. Applied research initiatives involving fungi extend broadly to areas of interest not only to industry but to agricultural and environmental sciences as well.It is this burgeoning interest in fungi as experimental systems for applied as well as basic research that has prompted publication of this series of books under the title The Mycota. This title knowingly relegates fungi into a separate realm, distinct from that of either plants, animals, or protozoa. For consistency throughout this series of volumes, the names adopted for major groups of fungi (representative genera in parentheses) are as follows:

These authors contributed equally to the manuscript.

The opportunistic pathogen Candida glabrata shows a concerning increase in drug resistance. Here, we present the analysis of two serial bloodstream isolates, obtained 12 days apart. Both isolates show pan-azole resistance and echinocandin resistance was acquired during the sampling interval. Genome sequencing identified nine nonsynonymous SNVs between the strains, including a S663P substitution in FKS2 and previously undescribed SNVs in MDE1 and FPR1, offering insight into how C. glabrata acquires drug resistance and adapts to a human host.

Blakeslea trispora displayed a very high transcript turnover in the gene for carotenoid cleavage dioxygenase, tsp3, during the sexual phase. An in vivo enzyme assay and chromatographic analysis led to the identification of ␤-apo-12=-carotenal as the first apocarotenoid involved in trisporic acid biosynthesis in B. trispora. Supplementation of C 18 trisporoids, namely D'orenone, methyl trisporate C, and trisporin C, increased tsp3 transcripts in the plus compared to minus partners. Interestingly, the tsp1 gene, which is involved in trisporic acid biosynthesis, was downregulated compared to tsp3 irrespective of asexual or sexual phase. Only the minus partners of both B. trispora and Mucor mucedo had enhanced ␤-carotene production after treatment with C 20 apocarotenoids, 15 different trisporoids, and their analogues. We conclude that the apocarotenoids and trisporoids influence gene transcription and metabolite production, depending upon the fungal strain, corresponding genus, and developmental phase, representing a "chemical dialect" during sexual communication. Mucorales fungi belonging to the subphylum incertae sedis Mucoromycotina (formerly classified in the class Zygomycetes) comprise 9 families, 51 genera, and around 205 species (1). These basal fungi are fast-growing soil saprotrophs that feed on dead and decaying organic matter. The asexual phase predominates their life cycle, with multinucleated haploid sporangiospores that germinate to mycelia of either the plus or minus mating type in heterothallic strains. Adversities, like environmental stresses or nutrient depletion, especially of nitrogen and phosphorus (2), lead to the sexual phase, in which complementary mating partners in close proximity exchange metabolites and form special aerial hyphae known as zygophores. The fusion of zygophores results in thousands of nuclei from both parents in the morphologically modified structure known as the progametangia. During further structural modifications and dormancy, which may extend from months to a year, most of the nuclei undergo degradation. Finally, gametangia bearing two nuclei from opposite partners fuse to form a thick-walled dikaryotic sexual spore known as the zygospore. Mitosis followed by meiosis results in four haploid products in a sporangium that develops from the zygospore (3). One Mucorales species in particular, Blakeslea trispora, has been commercially exploited for its potential to produce an excess of carotenoids, like ␤-carotene and lycopene, during its sexual phase of the life cycle (4, 5). According to a new report by Global Industrial Analysts, Inc., the worldwide market for carotenoids is projected to reach $1.3 billion by 2017. Hence, microbial carotenoids have been in the limelight as an ecofriendly sustainable alternative source for synthetics. Mucoralean carotenoids are not only under investigation for their biotechnological applications but also to help in understanding how they influence the sexual phase in those fungi.Apocarotenoids are the unsaturated nonpolar isoprenoids form...