The parasitic-neutral-mutual continuum of plant-fungal interactions

Interactions of plants with fungi are of imminent importance to crop production and thus for human nutrition. However, interactions range from pathogenic fungi, e.g. cereal rusts, to beneficial interactions with plant growth promotion through soil, endophytic or mycorrhizal fungi. Thus, mutually beneficial, neutral or parasitic/pathogenic interactions can be distinguished. In order to identify more general mechanisms on the fungal side coping with environmental and plant response associated stress, modern technologies are available including the -omics technologies. In addition to that, the comparison of the different interactions may be compared, both on a more general level, but also at very small scale to identify the different parameters guiding interchange of nutrients and signals. This will allow for a holistic view on plant health necessary to establish eco-friendly technologies also in crop protection and plant nutrition

Ectomycorrhizal Community Shifts at a Former Uranium Mining Site

Ectomycorrhizal communities at young oak, pine, and birch stands in a former uranium mining site showed a low diversity of morphotypes with a preference for contact and short-distance exploration strategies formed by the fungi Russulaceae , Inocybaceae , Cortinariaceae , Thelephoraceae , Rhizopogonaceae , Tricholomataceae , as well as abundant Meliniomyces bicolor . In order to have better control over abiotic conditions, we established pot experiments with re-potted trees taken from the sites of direct investigation. This more standardized cultivation resulted in a lower diversity and decreased prominence of M. bicolor . In addition, the exploration strategies shifted to include long-distance exploration types. To mimic secondary succession with a high prevalence of fungal propagules present in the soil, inoculation of re-potted trees observed under standardized conditions for two years was used. The super-inoculation increased the effect of lower abundance and diversity of morphotypes. The contact morphotypes correlated with high Al, Cu, Fe, Sr, and U soil contents, the dark-colored short-distance exploration type did not show a specific preference for soil characteristics, and the medium fringe type with rhizomorphs on oaks correlated with total nitrogen. Thus, we could demonstrate that field trees, in a species-dependent manner, selected for ectomycorrhizal fungi with exploration types are likely to improve the plant’s tolerance to specific abiotic conditions

An instant preparation method for nucleic acids of filamentous fungi

Preparation methods for both DNA and RNA of filamentous fungi often are labour intensive and unreliable. The rapid preparation protocol presented here has been found to work for Schizophyllum commune and other filamentous fungi

Geosmin synthase ges1 knock‐down by siRNA in the dikaryotic fungus Tricholoma vaccinum

Abstract Genetic manipulation for generating knock‐out experiments is essential in deciphering the precise function of a gene. However, dikaryotic fungi pose the inherent challenge of having two allelic versions of each gene, one in each nucleus. In addition, they often are slow‐growing and do not withstand protoplasting, which is why Agrobacterium tumefaciens ‐mediated transformation has been adapted. To obtain knock‐out strains, however, is not feasible with a mere deletion construct transformation and screening for deletions in both nuclear copies. Hence, a convenient method using chemically synthesized dicer substrate interfering RNA (DsiRNA) for posttranscriptional interference of targeted mRNA was developed, based on the fungal dicer/argonaute system inherent in fungi for sequence recognition and degradation. A proof‐of‐principle using this newly established method for knock‐down of the volatile geosmin is presented in the dikaryotic fungus Tricholoma vaccinum that is forming ectomycorrhizal symbiosis with spruce trees. The gene ges1 , a terpene synthase, was transcribed with a 50‐fold reduction in transcript levels in the knockdown strain. The volatile geosmin was slightly reduced, but not absent in the fungus carrying the knockdown construct pointing at low specificity in other terpene synthases known for that class of enzymes

What role might non-mating receptors play in Schizophyllum commune?

The B mating-type locus of the tetrapolar basidiomycete Schizophyllum commune encodes pheromones and pheromone receptors in multiple allelic specificities. This work adds substantial new evidence into the organization of the B mating-type loci of distantly related S. commune strains showing a high level of synteny in gene order and neighboring genes. Four pheromone receptor-like genes were found in the genome of S. commune with brl1, brl2 and brl3 located at the B mating-type locus, whereas brl4 is located separately. Expression analysis of brl genes in different developmental stages indicates a function in filamentous growth and mating. Based on the extensive sequence analysis and functional characterization of brl-overexpression mutants, a function of Brl1 in mating is proposed, while Brl3, Brl4 and Brl2 (to a lower extent) have a role in vegetative growth, possible determination of growth direction. The brl3 and brl4 overexpression mutants had a dikaryonlike, irregular and feathery phenotype, and they avoided the formation of same-clone colonies on solid medium, which points towards enhanced detection of self-signals. These data are supported by localization of Brl fusion proteins in tips, at septa and in not-yet-fused clamps of a dikaryon, confirming their importance for growth and development in S. commune

A stable backbone for the fungi

Fungi are abundant in the biosphere. They have fascinated mankind as far as written history goes and have considerably influenced our culture. In biotechnology, cell biology, genetics, and life sciences in general fungi constitute relevant model organisms. Once the phylogenetic relationships of fungi are stably resolved individual results from fungal research can be combined into a holistic picture of biology. However, and despite recent progress, the backbone of the fungal phylogeny is not yet fully resolved. Especially the early evolutionary history of fungi and the order or below-order relationships within the ascomycetes remain uncertain. Here we present the first phylogenomic study for a eukaryotic kingdom that merges all publicly available fungal genomes and expressed sequence tags (EST) to build a data set comprising 128 genes and 146 taxa. The resulting tree provides a stable phylogenetic backbone for the fungi. Moreover, we present the first formal supertree based on 161 fungal taxa and 128 gene trees. The combined evidences from the trees support the deep-level stability of the fungal groups towards a comprehensive natural system of the fungi. They indicate that the classification of the fungi, especially their alliance with the Microsporidia, requires careful revision. Our analysis is also an inventory of present day sequence information for the fungi. It provides insights into which phylogenenetic conclusions can and which cannot be drawn from the current data and may serve as a guide to direct further sequencing initiatives. Together with a comprehensive animal phylogeny, we provide the second of three pillars to understand the evolution of the multicellular eukaryotic kingdoms, fungi, metazoa, and plants, in the past 1.6 billion years

Organic acids, siderophores, enzymes and mechanical pressure for black slate bioweathering with the basidiomycete Schizophyllum commune

Although many fungi are known to be able to perform bioweathering of rocks and minerals, little information is available concerning the role of basidiomycetes in this process. The wood-rotting basidiomycete Schizophyllum commune was investigated for its ability to degrade black slate, a rock rich in organic carbon. Mechanical pressure of hyphae and extracellular polymeric substances was investigated for biophysical weathering. A mixed ß1-3/ß1-6 glucan, likely schizophyllan that is well known from S. commune, could be identified on black slate surfaces. Secretion of siderophores and organic acids as biochemical weathering agents was shown. Both may contribute to biochemical weathering in addition to enzymatic functions. Previously, the exoenzyme laccase was believed to attack organic the matter within the black slate, thereby releasing metals from the rock. Here, overexpression of laccase showed enhanced dissolution of quartz phases by etching and pitting. At the same time, the formation of a new secondary mineral phase, whewellite, could be demonstrated. Hence, a more comprehensive understanding of biophysical as well as biochemical weathering by S. commune could be reached and unexpected mechanisms like quartz dissolution linked to shale degradation. © 2019 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd

A Consistent Phylogenetic Backbone for the Fungi

The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses