Micro-scale Experimental System Coupled with Fluorescence-based Estimation of Fungal Biomass to Study Utilisation of Plant Substrates.

The degradation capacity and utilisation of complex plant substrates are crucial for the functioning of saprobic fungi and different plant symbionts with fundamental functions in ecosystems. Measuring the growth capacity and biomass of fungi on such systems is a challenging task. We established a new micro-scale experimental setup using substrates made of different plant species and organs as media for fungal growth. We adopted and tested a reliable and simple titration-based method for the estimation of total fungal biomass within the substrates using fluorescence-labelled lectin. We found that the relationship between fluorescence intensity and fungal dry weight was strong and linear but differed among fungi. The effect of the plant organ (i.e. root vs. shoot) used as substrate on fungal growth differed among plant species and between root endophytic fungal species. The novel microscale experimental system is useful for screening the utilisation of different substrates, which can provide insight into the ecological roles and functions of fungi. Furthermore, our fungal biomass estimation method has applications in various fields. As the estimation is based on the fungal cell wall, it measures the total cumulative biomass produced in a certain environment.

The new truffle genus Babosia and a new species of Stouffera from semiarid grasslands of Hungary.

Truffles with distinct morphological and anatomical features were collected during a study of hypogeous fungi of semiarid sandy grasslands of the Great Hungarian Plain in Hungary, representing the westernmost localities of the Eurasian steppe belt. None of the ascomata were collected near ectomycorrhizal plant species, and none were identified as ectomycorrhizal during previous surveys in the collection area. We studied morphoanatomical characteristics of these truffles with light and scanning electron microscopy and investigated their phylogenetic positions based on analyses of different nuclear loci. The truffles were found to represent two novel lineages that grouped with the Marcelleina-Peziza gerardii clade of the Pezizaceae. One formed a distinct lineage, for which we propose a new genus Babosia with a new species Babosia variospora characterized by diverse spore ornamentation varying even within one ascus. The truffles in the other lineage clustered with the rarely collected American truffle Stouffera longii and share with it similar spore ornamentation and habitat features. However, our material differs from S. longii by geographic origin, the quick and strong coloration of the ascomata to dark gray at cut surface or bruised area, varying spore number in asci, and smaller spore size; thus, we describe it as a new species, Stouffera gilkeyae.

Functional fine-tuning between bacterial DNA recombination initiation and quality control systems.

Homologous recombination (HR) is crucial for the error-free repair of DNA double-strand breaks (DSBs) and the restart of stalled replication. However, imprecise HR can lead to genome instability, highlighting the importance of HR quality control. After DSB formation, HR proceeds via DNA end resection and recombinase loading, whereas helicase-catalyzed disruption of a subset of subsequently formed DNA invasions is thought to be essential for maintaining HR accuracy via inhibiting illegitimate (non-allelic) recombination. Here we show that in vitro characterized mechanistic aberrations of E. coli RecBCD (resection and recombinase loading) RecQ (multifunctional DNA-restructuring helicase) mutant enzyme variants, on one hand, cumulatively deteriorate cell survival under certain conditions of genomic stress. On the other hand, we find that RecBCD and RecQ defects functionally compensate each other in terms of HR accuracy. The abnormally long resection and unproductive recombinase loading activities of a mutant RecBCD complex (harboring the D1080A substitution in RecB) cause enhanced illegitimate recombination. However, this compromised HR-accuracy phenotype is suppressed in double mutant strains harboring mutant RecQ variants with abnormally enhanced helicase and inefficient invasion disruptase activities. These results frame an in vivo context for the interplay of biochemical activities leading to illegitimate recombination, and underscore its long-range genome instability effects manifest in higher eukaryotes.

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi.

Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.