Complex and stable soil microbial networks are essential for productivity in plantation forestry, but their response to disturbances from harvesting and replanting is not well understood. This study assessed the impact of treatments designed to mitigate these disturbances on microbial biodiversity and networks in Eucalyptus plantation soils at three South African sites. We used high-throughput sequencing to catalogue fungal and bacterial biodiversity from 108 soil samples across three treatments: (i) retention of harvest residues (retained), (ii) removal of residues (removed), and (iii) removal of residues with added fertilizer (fertilized). Bioinformatic and statistical analyses of the sequence data revealed treatment-specific variations in microbial OTU richness, network structure and taxon associations at order-level. Microbiome richness was highest in 'retained' plots, and treatment-specific microbial diversity was evident in both fungal and bacterial communities. Network comparisons revealed that treatments to mitigate disturbances caused by harvesting significantly affected fungal networks but not bacterial networks. Fungal networks in 'retained' plots exhibited the highest complexity and stability compared to plots where the entire crop was removed. However, bacterial networks did not show significant differences in network structure among treatments. The associations between fungal and bacterial nodes were consistent in the three treatments, as indicated by similar Jaccard indices. However, distinct fungal hub nodes were found when comparing the 'retained' and 'removed' treatments. These findings highlight that retaining harvest residues enhances microbial richness and stabilizes fungal networks, making it a better strategy for managing soil disturbances than residue removal or fertilization.

Context Land use change can significantly affect plant-fungal interactions. Objectives We assessed how fungal endophytes within African wild olive ( Olea europaea subsp. cuspidata ) twigs are influenced by different levels of land use change and differences in surrounding vegetation types. Methods Twigs were sampled in the Western Cape Province (South Africa) and their fungal endophyte assemblages were characterised using culture-independent DNA metabarcoding. We assessed the effects of land use change (natural, semi-natural and planted (completely transformed)) and differences in surrounding vegetation types (grasses/low-growing plants versus shrubs/trees versus other olives) using fungal endophyte alpha and beta diversity measures. Co-occurrence networks were constructed to assess assemblage connectivity under different scenarios and to identify OTUs of potential ecological significance. Results OTU richness, but not abundance, was significantly influenced by both land use change and differences in the surrounding vegetation types. Planted African olives and those surrounded by heterospecific trees harboured the highest OTU richness. Only levels of land use change significantly influenced fungal endophyte assemblage composition. Specifically, fungal assemblages from natural habitats were distinct from those in planted and semi-natural habitats, which were similar to each other. Co-occurrence network analyses revealed that cohesive and species rich networks could only be maintained within the natural habitats. Conclusion These findings suggest that although the African olive is widespread, the identity and composition of their associated fungal assemblages are particularly sensitive to land use change. This study highlights the importance of conserving natural habitats, not just for the plants, but also for the maintenance of their associated fungal endophytes.

Patterns and drivers of succession provide insight into the mechanisms that govern community assembly, but remain poorly understood for microbial communities. We assess whether successional trends of trees are mirrored by foliar endophyte communities of three tree species across a deterministic woody successional gradient. Additionally, we test the relative contribution of abiotic predictors, biotic factors, and spatial distance between sites in predicting composition and richness of endophyte communities. Unlike the tree community, endophyte communities showed no consistent evidence of deterministic succession. Host identity was the most important factor structuring endophyte community composition; within hosts, spatial distance from the indigenous forest and between samples was important, while environmental predictors had small and inconsistent effects. Much variation in endophyte composition remained unexplained. In contrast, endophyte richness was well-explained by predictor variables. Host identity was most important in predicting endophyte richness, while the effect of other predictors on richness differed between host species. We conclude that deterministic succession in trees did not result in deterministic succession in endophyte communities; instead community assembly was most strongly influenced by host identity; while within hosts, neutral processes may be more important for endophyte assembly than deterministic factors.

Heat resistance is the ability to survive short, extreme temperature stresses, exceeding the own growth temperature by far. Despite their occurrence in natural substrates and their relevance for the food and healthcare industry, the diversity of fungi with heat resistance abilities is poorly studied. Sampling of boreal forest soils in Canada in combination with a heat-shock treatment (75 °C, 30 min) yielded, among others, four heat resistant, mesophilic fungal isolates. Based on rDNA barcode sequences, the novel isolates were assigned to Basidiomycota . In this study, we use macromorphological and micromorphological observations, cultivation assays and comparative genomics for physiological characterization, interspecific differentiation, and phylogenetic placement of these isolates. A phylogeny of 38 single-copy orthologous genes, an orthology analysis, and septal pore type analysis revealed the isolates as representatives of two new basidiomycetous species of the novel class Peribolosporomycetes , a sister lineage to all other members of Ustilaginomycotina . Further genomic and phenotypic data support two different species ( Peribolospora kevripleyi , Peribolospora baueri ), which are heat resistant and osmotolerant.

Host identity and location help shape fungal endophyte assemblages in plants. Hosts act as uptake filters from the environment and closely related hosts in the same location may harbour similar assemblages. We assessed the influence of host identity and geographic location on endophytic fungal assemblages within the native African olive and cultivated European olive in South Africa using high throughput sequencing. As hypothesised, the two hosts were found to share many endophytic species, but alpha diversity was lower within the European olive. The two hosts had significantly dissimilar endophyte assemblages. Distance between sites positively correlated with endophyte assemblage dissimilarities, demonstrating a strong effect of the surrounding environment on endophyte assemblages. African olive individuals had highly connected endophyte assemblages, unlike those within the European olive. Microbiome sharing and disconnected assemblages may have negative impacts on the health of the cultivated host.

Plantation forests have the potential to meet global economic and ecological objectives. The sustainability of plantations is influenced by a variety of above-and below-ground factors. Among these factors are soil-associated microbes, as they play a vital role in soil biogeochemical processes. However, when compared to natural forests, the microbial biodiversity associated with plantation soils is often less biodiverse due to anthropogenic distur-bances. The loss of microbial biodiversity in plantation soils can be partially mitigated through better post-harvest residue management regimes. To study this hypothesis in South African plantation soils, the effects of three post-harvest residue management regimes on fungal diversity were compared: retained, removed, or removed and fertilized. We collected 108 soil samples from these treatments at three study sites planted with a single Eucalyptus genotype. Consequently, DNA was extracted from all soil samples and fungal amplicon libraries were constructed using the Illumina MiSeq platform. The bioinformatic and statistical analyses of the data indicated that the post-harvest residue management regimes, the location of the study sites, and their interaction (soil treatment x site) influenced the community composition of soil fungi. The plots retaining post-harvest residues had a higher diversity of saprotrophs and symbiotrophs and fewer pathotrophs. The results showed that retaining post-harvest residue can improve the diversity of beneficial soil fungi in South African plantation soil. In the future, the South African and global forestry sectors should consider retaining post-harvest residues to ameliorate the tree and soil health of their plantations.

Activity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications so far mainly in biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from the thermophilic and lignocellulose-degrading white rot fungus Phanerochaete chrysosporium . By employing a comparative ABPP-based functional screen, including a direct profiling of wood substrate-bound enzymes, we identify those lignocellulose-degrading carbohydrate esterase (CE1 and CE15) and glycoside hydrolase (GH3, GH5, GH16, GH17, GH18, GH25, GH30, GH74 and GH79) enzymes specifically active in presence of the substrate. As expression of fungal enzymes remains challenging, our ABPP-mediated approach represents a preselection procedure for focusing experimental efforts on the most promising biocatalysts. Furthermore, this approach may also allow the functional annotation of domains-of-unknown functions (DUFs). The ABPP-based biocatalyst screening described here may thus allow the identification of active enzymes in a process of interest and the elucidation of novel biocatalysts that share no sequence similarity to known counterparts.

Fungal communities in above-ground tree tissues are hyperdiverse and are influenced by biotic interactions with other organisms living in or on these tissues. These biotic interactions are, however, still poorly understood. In this study, we aimed to understand how insect-associated gall formation on Eucalyptus foliage correlates with the diversity of foliar fungal communities in surrounding healthy leaf tissue, as well as the co-occurrence patterns among the members of the fungal community. We used ITS metabarcoding to characterise the foliar fungal communities of 179 individual E. grandis trees. These trees were assigned to infestation levels of the wasp Leptocybe invasa (Eulophidae: Hymenoptera), which causes gall formation on shoot tips and leaves of its host. Fungal community networks were calculated using a Pearson correlation coefficient. The composition and diversity of fungal communities were influenced by the severity of L. invasa infestations. We identified potential Eucalyptus pathogens with high sequence abundance at all disease severity levels, but network analysis indicated that the co-occurrence of potential pathogens between no to mild and medium to heavy infestation differed significantly. A better understanding of microbial interactions, especially the role of pathogens, can be useful for controlling disease- and beneficial host-associated microbial communities.

Thermophilic, thermotolerant and heat-resistant fungi developed different physiological traits, enabling them to sustain or even flourish under elevated temperatures, which are life-hostile for most other eukaryotes. With the growing demand of heat-stable molecules in biotechnology and industry, the awareness of heat-adapted fungi as a promising source of respective enzymes and biomolecules is still increasing. The aim of this study was to test two different strategies for the efficient isolation and identification of distinctly heat-adapted fungi from easily accessible substrates and locations. Eight compost piles and ten soil sites were sampled in combination with different culture-dependent approaches to describe suitable strategies for the isolation and selection of thermophilous fungi. Additionally, an approach with a heat-shock treatment, but without elevated temperature incubation led to the isolation of heat-resistant mesophilic species. The cultures were identified based on morphology, DNA barcodes, and microsatellite fingerprinting. In total, 191 obtained isolates were assigned to 31 fungal species, from which half are truly thermophilic or thermotolerant, while the other half are heat-resistant fungi. A numerous amount of heat-adapted fungi was isolated from both compost and soil samples, indicating the suitability of the used approaches and that the richness and availability of those organisms in such environments are substantially high.