Metal accumulation without enhanced oxalate secretion in wood degraded by brown rot fungi

Comparative Copper Resistance Strategies of Rhodonia placenta and Phanerochaete chrysosporium in a Copper/Azole-Treated Wood Microcosm

Copper-based formulations of wood preservatives are widely used in industry to protect wood materials from degradation caused by fungi. Wood treated with preservatives generate toxic waste that currently cannot be properly recycled. Despite copper being very efficient as an antifungal agent against most fungi, some species are able to cope with these high metal concentrations. This is the case for the brown-rot fungus Rhodonia placenta and the white-rot fungus Phanerochaete chrysosporium, which are able to grow efficiently in pine wood treated with Tanalith E3474. Here, we aimed to test the abilities of the two fungi to cope with copper in this toxic environment and to decontaminate Tanalith E-treated wood. A microcosm allowing the growth of the fungi on industrially treated pine wood was designed, and the distribution of copper between mycelium and wood was analysed within the embedded hyphae and wood particles using coupled X-ray fluorescence spectroscopy and Scanning Electron Microscopy (SEM)/Electron Dispersive Spectroscopy (EDS). The results demonstrate the copper biosorption capacities of P. chrysosporium and the production of copper-oxalate crystals by R. placenta. These data coupled to genomic analysis suggest the involvement of additional mechanisms for copper tolerance in these rot fungi that are likely related to copper transport (import, export, or vacuolar sequestration).

Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers

Fungi dominate the turnover of wood, Earth’s largest pool of aboveground terrestrial carbon. Fungi first evolved this capacity by degrading lignin to access and hydrolyze embedded carbohydrates (white rot). Multiple lineages, however, adapted faster reactive oxygen species (ROS) pretreatments to loosen lignocellulose and selectively extract sugars (brown rot). This brown rot “shortcut” often coincided with losses (>60%) of conventional lignocellulolytic genes, implying that ROS adaptations supplanted conventional pathways. We used comparative transcriptomics to further pursue brown rot adaptations, which illuminated the clear temporal expression shift of ROS genes, as well as the shift toward synthesizing more GHs in brown rot relative to white rot. These imply that gene regulatory shifts, not simply ROS innovations, were key to brown rot fungal evolution. These results not only reveal an important biological shift among these unique fungi, but they may also illuminate a trait that restricts brown rot fungi to certain ecological niches.

Fungi dominate the recycling of carbon sequestered in woody biomass. This process of organic turnover was first evolved among “white rot” fungi that degrade lignin to access carbohydrates and later evolved multiple times toward more efficient strategies to selectively target carbohydrates—“brown rot.” The brown rot adaption was often explained by mechanisms to deploy reactive oxygen species (ROS) to oxidatively attack wood structures. However, its genetic basis remains unclear, especially in the context of gene contractions of conventional carbohydrate-active enzymes (CAZYs) relative to white rot ancestors. Here, we hypothesized that these apparent gains in brown rot efficiency despite gene losses were due, in part, to upregulation of the retained genes. We applied comparative transcriptomics to multiple species of both rot types grown across a wood wafer to create a gradient of progressive decay and to enable tracking temporal gene expression. Dozens of “decay-stage-dependent” ortho-genes were isolated, narrowing a pool of candidate genes with time-dependent regulation unique to brown rot fungi. A broad comparison of the expression timing of CAZY families indicated a temporal regulatory shift of lignocellulose-oxidizing genes toward early stages in brown rot compared to white rot, enabling the segregation of oxidative treatment ahead of hydrolysis. These key brown rot ROS-generating genes with iron ion binding functions were isolated. Moreover, transcription energy was shifted to be invested on the retained GHs in brown rot fungi to strengthen carbohydrate conversion. Collectively, these results support the hypothesis that gene regulation shifts played a pivotal role in brown rot adaptation.

A genomics-informed study of oxalate and cellulase regulation by brown rot wood-degrading fungi

Wood-degrading fungi that selectively remove carbohydrates (brown rot) combine Fenton-based oxidation and enzymatic hydrolysis to degrade wood. These two steps are incompatible in close proximity. To explain this, brown rot fungi may stagger oxidative reactions ahead of hydrolysis, but the scale and environmental controls for such a mechanism have not been resolved in solid wood. Here, we focused on one reaction control parameter, oxalate. In coordination with Fe³⁺-reducing compounds (e.g., 2,5-dimethoxyhydroquinone), oxalate can either promote Fenton chemistry by mobilizing Fe³⁺ as mono-oxalates (facilitative) or inhibit Fenton chemistry (protective) by restricting reducibility and the formation of Fenton's reagent as Fe³⁺/Fe²-(oxalate)_2,3. Here, we sectioned wood wafers colonized directionally by Postia placenta and Gloeophyllum trabeum to map end-to-end the expression of oxalate synthesis genes and to overlay enzyme activities, metabolites, and wood modifications. Near advancing hyphal fronts, oxaloacetase expression was up upregulated for both fungi, while regulation patterns of paralogous of isocitrate lyases and glyoxylate dehydrogenases varied, suggesting different physiological roles. Oxalate decarboxylase (ODC) expression in G. trabeum was induced in more decayed wood behind the hyphal front, but was constitutively expressed in all P. placenta sections. Relative ODC activities increased and oxalate levels stabilized in more decayed wood behind the hyphal front. Endoglucanase (EG) activity, on the other hand, peaked for both fungi in later decay stages. These oxalate optimization patterns are in line with previous whole-block 'spiking' experiments tracking oxalate, but we provide here information on its genetic controls across a spatial gradient. As a complement, we also demonstrate in vitro the plausibility of a protective role for oxalate, to emphasize that these fungi might be optimizing oxalate at a given level to maximize Fenton reactions but to minimize oxidative damage.

Fungal accumulation of metals from building materials during brown rot wood decay

This study analyzes the accumulation and translocation of metal ions in wood during the degradation performed by one strain of each of the three brown rot fungi; Serpula lacrymans, Meruliporia incrassata and Coniophora puteana. These fungi species are inhabitants of the built environment where the prevention and understanding of fungal decay is of high priority. This study focuses on the influence of various building materials in relation to fungal growth and metal uptake. Changes in the concentration of iron, manganese, calcium and copper ions in the decayed wood were analyzed by induced coupled plasma spectroscopy and related to wood weight loss and oxalic acid accumulation. Metal transport into the fungal inoculated wood was found to be dependent on the individual strain/species. The S. lacrymans strain caused a significant increase in total iron whereas the concentration of copper ions in the wood appeared decreased after 10 weeks of decay. Wood inoculated with the M. incrassata isolate showed the contrary tendency with high copper accumulation and low iron increase despite similar weight losses for the two strains. However, significantly lower oxalic acid accumulation was recorded in M. incrassata degraded wood. The addition of a building material resulted in increased weight loss in wood degraded by C. puteana in the soil-block test; however, this could not be directly linked specifically to the accumulation of any of the four metals recorded. The accumulation of oxalic acid seemed to influence the iron uptake. The study assessing the influence of the presence of soil and glass in the soil-block test revealed that soil contributed the majority of the metals for uptake by the fungi and contributed to increased weight loss. The varying uptake observed among the three brown rot fungi strains toward the four metals analyzed may be related to the specific non-enzymatic and enzymatic properties including bio-chelators employed by each of the species during wood decay.

Synergy between pretreatment lignocellulose modifications and saccharification efficiency in two brown rot fungal systems

Brown rot wood-degrading fungi distinctly modify lignocellulose and completely hydrolyze polysaccharides (saccharification), typically without secreting an exo-acting glucanase and without removing lignin. Although each step of this two-step approach evolved within the same organism, it is unknown if the early lignocellulose modifications are made to specifically facilitate their own abbreviated enzyme system or if enhancements are more general. Because commercial pretreatments are typically approached as an isolated step, answering this question has immense implication on bioprocessing. We pretreated spruce and pine blocks with one of two brown rot fungi, Gloeophyllum trabeum or Fomitopsis pinicola. Wood harvested at weeks 1, 2, 4, and 8 showed a progression of weight loss from time zero due to selective carbohydrate removal. Hemicellulose losses progressed faster than cellulose loss. This "pretreated" material was then saccharified with commercially relevant Trichoderma reesei cellulases or with cellulases from the brown rot fungi responsible for degrading the wood to test for synergy. With increased decay, a significant increase in saccharification efficiency was apparent but not limited to same-species enzyme sources. We also calculated total sugar yields, and calculations that compensate for sugars consumed by fungi suggest a shorter residence time for fungal colonization than calculations based solely on saccharification yields.

Geomycology: biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bioweathering and bioremediation

The study of the role that fungi have played and are playing in fundamental geological processes can be termed 'geomycology' and this article seeks to emphasize the fundamental importance of fungi in several key areas. These include organic and inorganic transformations and element cycling, rock and mineral transformations, bioweathering, mycogenic mineral formation, fungal-clay interactions, metal-fungal interactions, and the significance of such processes in the environment and their relevance to areas of environmental biotechnology such as bioremediation. Fungi are intimately involved in biogeochemical transformations at local and global scales, and although such transformations occur in both aquatic and terrestrial habitats, it is the latter environment where fungi probably have the greatest influence. Within terrestrial aerobic ecosystems, fungi may exert an especially profound influence on biogeochemical processes, particularly when considering soil, rock and mineral surfaces, and the plant root-soil interface. The geochemical transformations that take place can influence plant productivity and the mobility of toxic elements and substances, and are therefore of considerable socio-economic relevance, including human health. Of special significance are the mutualistic symbioses, lichens and mycorrhizas. Some of the fungal transformations discussed have beneficial applications in environmental biotechnology, e.g. in metal leaching, recovery and detoxification, and xenobiotic and organic pollutant degradation. They may also result in adverse effects when these processes are associated with the degradation of foodstuffs, natural products, and building materials, including wood, stone and concrete. It is clear that a multidisciplinary approach is essential to understand fully all the phenomena encompassed within geomycology, and it is hoped that this review will serve to catalyse further research, as well as stimulate interest in an area of mycology of global significance.