Investigation of growth responses in saprophytic fungi to charred biomass

We present the results of a study testing the response of two saprophytic white-rot fungi species, Pleurotus pulmonarius and Coriolus versicolor, to charred biomass (charcoal) as a growth substrate. We used a combination of optical microscopy, scanning electron microscopy, elemental abundance measurements, and isotope ratio mass spectrometry (<sup>13</sup>C and <sup>15</sup>N) to investigate fungal colonisation of control and incubated samples of Scots Pine (Pinus sylvestris) wood, and charcoal from the same species produced at 300 °C and 400 °C. Both species of fungi colonise the surface and interior of wood and charcoals over time periods of less than 70 days; however, distinctly different growth forms are evident between the exterior and interior of the charcoal substrate, with hyphal penetration concentrated along lines of structural weakness. Although the fungi were able to degrade and metabolise the pine wood, charcoal does not form a readily available source of fungal nutrients at least for these species under the conditions used in this study

Critical Assessment of Metagenome Interpretation:A benchmark of metagenomics software

International audienceIn metagenome analysis, computational methods for assembly, taxonomic profilingand binning are key components facilitating downstream biological datainterpretation. However, a lack of consensus about benchmarking datasets andevaluation metrics complicates proper performance assessment. The CriticalAssessment of Metagenome Interpretation (CAMI) challenge has engaged the globaldeveloper community to benchmark their programs on datasets of unprecedentedcomplexity and realism. Benchmark metagenomes were generated from newlysequenced ~700 microorganisms and ~600 novel viruses and plasmids, includinggenomes with varying degrees of relatedness to each other and to publicly availableones and representing common experimental setups. Across all datasets, assemblyand genome binning programs performed well for species represented by individualgenomes, while performance was substantially affected by the presence of relatedstrains. Taxonomic profiling and binning programs were proficient at high taxonomicranks, with a notable performance decrease below the family level. Parametersettings substantially impacted performances, underscoring the importance ofprogram reproducibility. While highlighting current challenges in computationalmetagenomics, the CAMI results provide a roadmap for software selection to answerspecific research questions

White-Rot Fungi in Bioremediation

Bioremediation is defined as the application of biological processes to the treatment of pollution. Most research on the field of bioremediation has focused on bacteria, and fungal bioremediation (mycoremediation) has also been attracting the interest just for a couple of decades. The toxicity of many pollutants reduces natural attenuation of bacteria, but white-rot fungi (WRF) can challenge with toxic levels of the most pollutants. Fungi are robust organisms having very high tolerance to toxic environments, and this feature makes them ideal to use for bioremedial purposes. White-rot fungi are basidiomycetes that are capable of degrading a lignocellulose substrate. Extracellular enzymes involved in the degradation of lignin and xenobiotics by white-rot fungi include several kinds of laccases, peroxidases, and oxidases producing H2O2. Nowadays, great progress in this area may derive from modern molecular technologies, which may provide cheaper potential sources of various enzymes by means of genetically modified microorganisms or plants. This chapter explains the bioremediation and its application conditions and degradation mechanisms of the harmful compounds such as textile dyes, PAHs, chlorophenols, TNT, pesticides, and nylon