Plant microbiomes are critical to host adaptation and impact plant productivity and health. Root-associated microbiomes vary by soil and host genotype, but the contribution of these factors to community structure and metabolic potential has not been fully addressed. Here we characterize root microbial communities of two disparate agricultural crops grown in the same natural soil in a controlled and replicated experimental system. Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. Root colonization requires multiple functional capabilities, and these capabilities are enriched at the community level. Differences between the root-associated microbial communities from different plants are observed at the genus or species level, and are related to root-zone environmental factors.

Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium . Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium , respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli , the enzymes were shown to oxidize high redox potential substrates, but not Mn 2+ . Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium .

Composting of municipal solid waste (MSW) was studied in an attempt to elaborate transformations of organic matter (OM) during the process and define parameters for the degree of maturity of the product. Composting was performed in 1‐m3 plastic boxes and the following parameters were measured in 13 samples during 132 d of composting: temperature, C/N ratio, ash content, humic substance contents, and fractions (humic acid, fulvic acid, and nonhumic fraction‐HA, FA, and NHF, respectively). Spectroscopic methods (CPMAS 13C‐NMR, DRIFT) were used to study the chemical composition of the OM. A bioassay based on growth of cucumber (Cucumis sativus L. cv. Dlila) plants was correlated to other parameters. The C/N ratio and ash content showed a typical high rate of change during the first 60 d and reached a plateau thereafter. The HA content increased to a maximum at 112 d, corresponding to the highest plant dry weight and highest 1650/1560 (cm−1/cm−1) peak ratios calculated from DRIFT spectra. 13C‐NMR and DRIFT spectra of samples taken from the composting MSW during the process showed that the residual OM contained an increasing level of aromatic structures. Plant‐growth bioassay, HA content, and the DRIFT spectra indicated that MSW compost described in this study, stabilized and achieved maturity after about 110 d.

Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition from our petroleum-based economy into a bio-based circular economy and has the ability to sustainably produce resilient sources of food, feed, chemicals, fuels, textiles, and materials for construction, automotive and transportation industries, for furniture and beyond. Fungal biotechnology offers solutions for securing, stabilizing and enhancing the food supply for a growing human population, while simultaneously lowering greenhouse gas emissions. Fungal biotechnology has, thus, the potential to make a significant contribution to climate change mitigation and meeting the United Nation's sustainable development goals through the rational improvement of new and established fungal cell factories. The White Paper presented here is the result of the 2nd Think Tank meeting held by the EUROFUNG consortium in Berlin in October 2019. This paper highlights discussions on current opportunities and research challenges in fungal biotechnology and aims to inform scientists, educators, the general public, industrial stakeholders and policymakers about the current fungal biotech revolution.

Humic substances (HS) were extracted from separated cattle‐manure compost (CSM) at various stages of decomposition. Carbon‐13 nuclear magnetic resonance (13C‐NMR) and Fourier‐transform infrared (FTIR) spectroscopy measurements were performed on the purified humic acids (HA) as well as crude fiber and chemical analyses. Levels of HS extracted from the CSM samples doubled during the composting (from 377 to 710 g kg−1 organic matter [OM]). The HS were divided into: (i) HA, which increased from 184 to 457 g kg−1 OM; and (ii) a fulvic fraction (FF). The FF was separated on XAD‐8 resin to: (i) fulvic acid (FA), which maintained an unchanged level during composting (80–100 g kg−1); and (ii) a nonhumic fraction (NHF), which increased from 107 to 170 g kg−1 OM during the process. The ratios between the concentrations of these fractions were tested as humification indexes. These indexes changed significantly during the process and were found to correlate exponentially with the composting time, C/N ratio, or both. Quantities of low‐molecular‐weight components (FF and NHF) rapidly increased during the first 40 d of composting and were nearly constant thereafter. The HA and HS contents reached nearly constant values after ∼90 d. Only slight compositional and structural changes in CSM HA were detected with cross‐polarization magic‐angle spinning (CPMAS) 13C‐NMR, FTIR spectra, and chemical analyses. The elemental composition and functional groups of CSM HA resembled those reported for HA of plant residues, peats, and incompletely humified materials. The CPMAS 13C‐NMR spectra of the CSM HA resembled that of lignin. The aromaticity of the HA was about 40% and the lignin content was approximately 60%. The NMR data correlated well with results obtained by FTIR spectroscopy, both indicating that the CSM HA are composed of partially degraded constituents of plant tissue, which still retain to some extent their chemical structures. The major plant components identified in the HA were lignin, carbohydrates, and long‐chain aliphatic structural groups.