• Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

      Lücking, Robert; Aime, M Catherine; Robbertse, Barbara; Miller, Andrew N; Ariyawansa, Hiran A; Aoki, Takayuki; Cardinali, Gianluigi; Crous, Pedro W; Druzhinina, Irina S; Geiser, David M; et al. (BMC, 2020-07-10)
      True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
    • An unprecedented spiro [furan-2,1’-indene]-3-one derivative and other nematicidal and antimicrobial metabolites from Sanghuangporus sp. (Hymenochaetaceae, Basidiomycota) collected in Kenya

      Chepkirui, Clara; Cheng, Tian; Matasyoh, Josphat; Decock, Cony; Stadler, Marc; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.
      Bioassay guided fractionation of extracts derived from submerged cultures of a Sanghuangporus sp. (i.e., the genus that was until recently referred to as the “Inonotus linteus complex” of medicinal mushrooms) originating from Kenya led to the isolation of a new spiro [furan-2,1’-indine]-3-one derivative, for which we propose the trivial name phelligridin L (1) together with the known compounds 3,14′-bihispidinyl (2), hispidin (3), ionylideneacetic acid (4), 1S-(2E)-5-[(1R)-2,2-dimethyl-6-methylidenecyclohexyl]-3-methylpent-2-enoic acid (5), phellidine E (6) and phellidine D (7). Compounds 1–3, showed moderate nematicidal activity against Caenorhabditis elegans with LD50 of 12.5 μg/m. The nematicidal activity of 3, 14′-bihispidinyl and hispidin (1, 2) has not been reported before. Furthermore, compounds 1–5 demonstrated moderate antimicrobial activity against various test organisms.
    • Unsaturated Fatty Acids Control Biofilm Formation of and Other Gram-Positive Bacteria.

      Yuyama, Kamila Tomoko; Rohde, Manfred; Molinari, Gabriella; Stadler, Marc; Abraham, Wolf-Rainer; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (MDPI, 2020-11-08)
      Infections involving biofilms are difficult to treat due to increased resistances against antibiotics and the immune system. Hence, there is an urgent demand for novel drugs against biofilm infections. During our search for novel biofilm inhibitors from fungi, we isolated linoleic acid from the ascomycete Hypoxylon fragiforme which showed biofilm inhibition of several bacteria at sub-MIC concentrations. Many fatty acids possess antimicrobial activities, but their minimum inhibitory concentrations (MIC) are high and reports on biofilm interferences are scarce. We demonstrated that not only linoleic acid but several unsaturated long-chain fatty acids inhibited biofilms at sub-MIC concentrations. The antibiofilm activity exerted by long-chain fatty acids was mainly against Gram-positive bacteria, especially against Staphylococcus aureus. Micrographs of treated S. aureus biofilms revealed a reduction in the extracellular polymeric substances, pointing to a possible mode of action of fatty acids on S. aureus biofilms. The fatty acids had a strong species specificity. Poly-unsaturated fatty acids had higher activities than saturated ones, but no obvious rule could be found for the optimal length and desaturation for maximal activity. As free fatty acids are non-toxic and ubiquitous in food, they may offer a novel tool, especially in combination with antibiotics, for the control of biofilm infections.
    • Viridistratins A-C, Antimicrobial and Cytotoxic Benzo[]fluoranthenes from Stromata of (Hypoxylaceae, Ascomycota).

      Becker, Kevin; Wessel, Anna-Charleen; Luangsa-Ard, J Jennifer; Stadler, Marc; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (MDPI, 2020-05-23)
      During the course of our search for novel biologically active metabolites from tropical fungi, we are using chemotaxonomic and taxonomic methodology for the preselection of interesting materials. Recently, three previously undescribed benzo[j]fluoranthenes (1-3) together with the known derivatives truncatones A and C (4, 5) were isolated from the stromata of the recently described species Annulohypoxylon viridistratum collected in Thailand. Their chemical structures were elucidated by means of spectral methods, including nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry (HR-MS). The new compounds, for which we propose the trivial names viridistratins A-C, exhibited weak-to-moderate antimicrobial and cytotoxic activities in cell-based assays.
    • Viriditins from Byssochlamys spectabilis, their stereochemistry and biosynthesis

      López-Fernández, Sebastián; Campisano, Andrea; Schulz, Barbara J.; Steinert, Michael; Stadler, Marc; Surup, Frank; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (Elsevier, 2020-01-30)
    • Volatiles from the hypoxylaceous fungi and Hypoxylon macrocarpum.

      Rinkel, Jan; Babczyk, Alexander; Wang, Tao; Stadler, Marc; Dickschat, Jeroen S; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (2018-01-01)
      The volatiles emitted by the ascomycetes Hypoxylon griseobrunneum and Hypoxylon macrocarpum (Hypoxylaceae, Xylariales) were collected by use of a closed-loop stripping apparatus (CLSA) and analysed by GC-MS. The main compound class of both species were polysubstituted benzene derivatives. Their structures could only be unambiguously determined by comparison to all isomers with different substitution patterns. The substitution pattern of the main compound from H. griseobrunneum, the new natural product 2,4,5-trimethylanisole, was explainable by a polyketide biosynthesis mechanism that was supported by a feeding experiment with (methyl-2H3)methionine.
    • Volatiles from the tropical ascomycete (Hypoxylaceae, Xylariales).

      Wang, Tao; Mohr, Kathrin I; Stadler, Marc; Dickschat, Jeroen S; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany (Beilstein Institut, 2018-01-01)
      The volatiles from the fungus Daldinia clavata were collected by use of a closed-loop stripping apparatus and analysed by GC-MS. A few compounds were readily identified by comparison of measured to library mass spectra and of retention indices to published data, while for other compounds a synthesis of references was required. For one of the main compounds, 5-hydroxy-4,6-dimethyloctan-3-one, the relative and absolute configuration was determined by synthesis of all eight stereoisomers and gas chromatographic analysis using a homochiral stationary phase. Another identified new natural product is 6-nonyl-2H-pyran-2-one. The antimicrobial and cytotoxic effects of the synthetic volatiles are also reported.
    • Volatiles from the xylarialean fungus .

      Dickschat, Jeroen S; Wang, Tao; Stadler, Marc; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.
      The volatiles emitted by agar plate cultures of the xylarialean fungus were investigated by use of a closed loop stripping apparatus in combination with GC-MS. Several aromatic compounds were found that could only be identified by comparison to all possible constitutional isomers with different ring substitution patterns. For the set of identified compounds a plausible biosynthetic scheme was suggested that gives further support for the assigned structures.
    • Yeast diversity and species recovery rates from beech forest soils

      Yurkov, Andrey M.; Wehde, Thorsten; Federici, Julian; Schäfer, Angela M.; Ebinghaus, Malte; Lotze-Engelhard, Sascha; Mittelbach, Moritz; Prior, René; Richter, Christian; Röhl, Oliver; et al. (2016-07-14)