Global field collection data confirm an affinity of brown rot fungi for coniferous habitats and substrates.

Unlike 'white rot' (WR) wood-decomposing fungi that remove lignin to access cellulosic sugars, 'brown rot' (BR) fungi selectively extract sugars and leave lignin behind. The relative frequency and distribution of these fungal types (decay modes) have not been thoroughly assessed at a global scale; thus, the fate of one-third of Earth's aboveground carbon, wood lignin, remains unclear. Using c. 1.5 million fungal sporocarp and c. 30 million tree records from publicly accessible databases, we mapped and compared decay mode and tree type (conifer vs angiosperm) distributions. Additionally, we mined fungal record metadata to assess substrate specificity per decay mode. The global average for BR fungi proportion (BR/(BR + WR records)) was 13% and geographic variation was positively correlated (R2 = 0.45) with conifer trees proportion (conifer/(conifer + angiosperm records)). Most BR species (61%) were conifer, rather than angiosperm (22%), specialists. The reverse was true for WR (conifer: 19%; angiosperm: 62%). Global BR proportion patterns were predicted with greater accuracy using the relative distributions of individual tree species (R2 = 0.82), rather than tree type. Fungal decay mode distributions can be explained by tree type and, more importantly, tree species distributions, which our data suggest is due to strong substrate specificities.

The 2022 FASEB Virtual Catalyst Conference on the Cardiac Interatrial Septum and Stroke Risk, December 7, 2022.

There is emerging evidence that the cardiac interatrial septum has an important role as a thromboembolic source for ischemic strokes. There is little consensus on treatment of patients with different cardiac interatrial morphologies or pathologies who have had stroke. In this paper, we summarize the important background, diagnostic, and treatment considerations for this patient population as presented during the Federation of American Societies for Experimental Biology (FASEB) Virtual Catalytic Conference on the Cardiac Interatrial Septum and Stroke Risk, held on December 7, 2022. During this conference, many aspects of the cardiac interatrial septum were discussed. Among these were the embryogenesis of the interatrial septum and development of anatomic variants such as patent foramen ovale and left atrial septal pouch. Also addressed were various mechanisms of injury such as shunting physiologies and the consequences that can result from anatomic variants, as well as imaging considerations in echocardiography, computed tomography, and magnetic resonance imaging. Treatment options including anticoagulation and closure were addressed, as well as an in-depth discussion on whether the left atrial septal pouch is a stroke risk factor. These issues were discussed and debated by multiple experts from neurology, cardiology, and radiology.

A Laccase Gene Reporting System That Enables Genetic Manipulations in a Brown Rot Wood Decomposer Fungus Gloeophyllum trabeum.

Brown rot fungi are primary decomposers of wood and litter in northern forests. Relative to other microbes, these fungi have evolved distinct mechanisms that rapidly depolymerize and metabolize cellulose and hemicellulose without digesting the more recalcitrant lignin. Its efficient degradative system has therefore attracted considerable attention for the development of sustainable biomass conversion technologies. However, there has been a significant lack of genetic tools in brown rot species by which to manipulate genes for both mechanistic studies and engineering applications. To advance brown rot genetic studies, we provided a gene-reporting system that can facilitate genetic manipulations in a model fungus Gloeophyllum trabeum. We first optimized a transformation procedure in G. trabeum, and then transformed the fungus into a constitutive laccase producer with a well-studied white rot laccases gene (from Trametes versicolor). With this, we built a gene reporting system based on laccase gene's expression and its rapid assay using an 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) indicator dye. The laccase reporter system was validated robust enough to allow us to test the effects of donor DNA's formats, protoplast viability, and gene regulatory elements on transformation efficiencies. Going forward, we anticipate the toolset provided in this work would expedite phenotyping studies and genetic engineering of brown rot species. IMPORTANCE One of the most ubiquitous types of decomposers in nature, brown rot fungi, has lacked robust genetic tools by which to manipulate genes and understand its biology. Brown rot fungi are primary decomposers in northern forests helping recycle the encased carbons in trees back to ecosystem. Relative to other microbes, these fungi employ distinctive mechanisms to disrupt and consume the lignified polysaccharides in wood. Its decay mechanism allows fast, selective carbohydrate catabolization, but without digesting lignin-a barren component that produces least energy trade back for fungal metabolisms. Thus, its efficient degradative system provides a great platform for developing sustainable biotechnologies for biomass conversions. However, progress has been hampered by the lack genetic tools facilitating mechanistic studies and engineering applications. Here, the laccase reporter system provides a genetic toolset for genetic manipulations in brown rot species, which we expect would advance relevant genetic studies for discovering and harnessing the unique fungal degradative mechanisms.

Proteome of the Wood Decay Fungus Fomitopsis pinicola Is Altered by Substrate.

The brown rot fungus Fomitopsis pinicola efficiently depolymerizes wood cellulose via the combined activities of oxidative and hydrolytic enzymes. Mass spectrometric analyses of culture filtrates identified specific proteins, many of which were differentially regulated in response to substrate composition.

Diversity of genomic adaptations to the post-fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual development.

Wildfires drastically impact the soil environment, altering the soil organic matter, forming pyrolyzed compounds, and markedly reducing the diversity of microorganisms. Pyrophilous fungi, especially the species from the orders Pezizales and Agaricales, are fire-responsive fungal colonizers of post-fire soil that have historically been found fruiting on burned soil and thus may encode mechanisms of processing these compounds in their genomes. Pyrophilous fungi are diverse. In this work, we explored this diversity and sequenced six new genomes of pyrophilous Pezizales fungi isolated after the 2013 Rim Fire near Yosemite Park in California, USA: Pyronema domesticum, Pyronema omphalodes, Tricharina praecox, Geopyxis carbonaria, Morchella snyderi, and Peziza echinospora. A comparative genomics analysis revealed the enrichment of gene families involved in responses to stress and the degradation of pyrolyzed organic matter. In addition, we found that both protein sequence lengths and G + C content in the third base of codons (GC3) in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi. A comparative transcriptome analysis of P. domesticum under two conditions - growing on charcoal, and during sexual development - identified modules of genes that are co-expressed in the charcoal and light-induced sexual development conditions. In addition, environmental sensors such as transcription factors STE12, LreA, LreB, VosA, and EsdC were upregulated in the charcoal condition. Taken together, these results highlight genomic adaptations of pyrophilous fungi and indicate a potential connection between charcoal tolerance and fruiting body formation in P. domesticum.

Capturing an Early Gene Induction Event during Wood Decay by the Brown Rot Fungus Rhodonia placenta.

Brown rot fungi dominate wood decomposition in coniferous forests, and their carbohydrate-selective mechanisms are of commercial interest. Brown rot was recently described as a two-step, sequential mechanism orchestrated by fungi using differentially expressed genes (DEGs) and consisting of oxidation via reactive oxygen species (ROS) followed by enzymatic saccharification. There have been indications, however, that the initial oxidation step itself might require induction. To capture this early gene regulation event, here, we integrated fine-scale cryosectioning with whole-transcriptome sequencing to dissect gene expression at the single-hyphal-cell scale (tens of micrometers). This improved the spatial resolution 50-fold, relative to previous work, and we were able to capture the activity of the first 100 µm of hyphal front growth by Rhodonia placenta in aspen wood. This early decay period was dominated by delayed gene expression patterns as the fungus ramped up its mechanism. These delayed DEGs included many genes implicated in ROS pathways (lignocellulose oxidation [LOX]) that were previously and incorrectly assumed to be constitutively expressed. These delayed DEGs, which include those with and without predicted functions, also create a focused subset of target genes for functional genomics. However, this delayed pattern was not universal, with a few genes being upregulated immediately at the hyphal front. Most notably, this included a gene commonly implicated in hydroquinone and iron redox cycling: benzoquinone reductase. IMPORTANCE Earth's aboveground terrestrial biomass is primarily wood, and fungi dominate wood decomposition. Here, we studied these fungal pathways in a common "brown rot"-type fungus, Rhodonia placenta, that selectively extracts sugars from carbohydrates embedded within wood lignin. Using a space-for-time design to map fungal gene expression at the extreme hyphal front in wood, we made two discoveries. First, we found that many genes long assumed to be "on" (constitutively expressed) from the very beginning of decay were instead "off" before being upregulated, when mapped (via transcriptome sequencing [RNA-seq]) at a high resolution. Second, we found that the gene encoding benzoquinone reductase was "on" in incipient decay and quickly downregulated, implying a key role in "kick-starting" brown rot.

Distinctive carbon repression effects in the carbohydrate-selective wood decay fungus Rhodonia placenta.

Brown rot fungi dominate the carbon degradation of northern terrestrial conifers. These fungi adapted unique genetic inventories to degrade lignocellulose and to rapidly release a large quantity of carbohydrates for fungal catabolism. We know that brown rot involves "two-step" gene regulation to delay most hydrolytic enzyme expression until after harsh oxidative pretreatments. This implies the crucial role of concise gene regulation to brown rot efficacy, but the underlying regulatory mechanisms remain uncharacterized. Here, using the combined transcriptomic and enzyme analyses we investigated the roles of carbon catabolites in controlling gene expression in model brown rot fungus Rhodonia placenta. We identified co-regulated gene regulons as shared transcriptional responses to no-carbon controls, glucose, cellobiose, or aspen wood (Populus sp.). We found that cellobiose, a common inducing catabolite for fungi, induced expression of main chain-cleaving cellulases in GH5 and GH12 families (cellobiose vs. no-carbon > 4-fold, Padj < 0.05), whereas complex aspen was a universal inducer for Carbohydrate Active Enzymes (CAZymes) expression. Importantly, we observed the attenuated glucose-mediated repression effects on cellulases expression, but not on hemicellulases and lignin oxidoreductases, suggesting fungi might have adapted diverged regulatory routes to boost cellulase production for the fast carbohydrate release. Using carbon regulons, we further predicted the cis- and trans-regulatory elements and assembled a network model of the distinctive regulatory machinery of brown rot. These results offer mechanistic insights into the energy efficiency traits of a common group of decomposer fungi with enormous influence on the carbon cycle.

Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms.

Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth's woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps  of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.

Using MALDI-FTICR-MS Imaging to Track Low-Molecular-Weight Aromatic Derivatives of Fungal Decayed Wood.

Low-molecular-weight (LMW) aromatics are crucial in meditating fungal processes for plant biomass decomposition. Some LMW compounds are employed as electron donors for oxidative degradation in brown rot (BR), an efficient wood-degrading strategy in fungi that selectively degrades carbohydrates but leaves modified lignins. Previous understandings of LMW aromatics were primarily based on "bulk extraction", an approach that cannot fully reflect their real-time functions during BR. Here, we applied an optimized molecular imaging method that combines matrix-assisted laser desorption ionization (MALDI) with Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) to directly measure the temporal profiles of BR aromatics as Rhodonia placenta decayed a wood wafer. We found that some phenolics were pre-existing in wood, while some (e.g., catechin-methyl ether and dihydroxy-dimethoxyflavan) were generated immediately after fungal activity. These pinpointed aromatics might be recruited to drive early BR oxidative mechanisms by generating Fenton reagents, Fe2+ and H2O2. As BR progressed, ligninolytic products were accumulated and then modified into various aromatic derivatives, confirming that R. placenta depolymerizes lignin. Together, this work confirms aromatic patterns that have been implicated in BR fungi, and it demonstrates the use of MALDI-FTICR-MS imaging as a new approach to monitor the temporal changes of LMW aromatics during wood degradation.

A Fungal Secretome Adapted for Stress Enabled a Radical Wood Decay Mechanism.

Brown rot fungi release massive amounts of carbon from forest deadwood, particularly at high latitudes. These fungi degrade wood by generating small reactive oxygen species (ROS) to loosen lignocellulose, to then selectively remove carbohydrates. The ROS mechanism has long been considered the key adaptation defining brown rot wood decomposition, but recently, we found preliminary evidence that fungal glycoside hydrolases (GHs) implicated in early cell wall loosening might have been adapted to tolerate ROS stress and to synergize with ROS to loosen woody lignocellulose. In the current study, we found more specifically that side chain hemicellulases that help in the early deconstruction of the lignocellulosic complex are significantly more tolerant of ROS in the brown rot fungus Rhodonia placenta than in a white rot fungus (Trametes versicolor) and a soft rot fungus (Trichoderma reesei). Using proteomics to understand the extent of tolerance, we found that significant oxidation of secreted R. placenta proteins exposed to ROS was less than half of the oxidation observed for T. versicolor or T. reesei. The principal oxidative modifications observed in all cases were monooxidation and dioxidation/trioxidation (mainly in methionine and tryptophan residues), some of which were critical for enzyme activity. At the peptide level, we found that GHs in R. placenta were the least ROS affected among our tested fungi. These results confirm and describe underlying mechanisms of tolerance in early-secreted brown rot fungal hemicellulases. These enzymatic adaptations may have been as important as nonenzymatic ROS pathway adaptations in brown rot fungal evolution. IMPORTANCE Brown rot fungi play a critical role in carbon recycling and are of industrial interest. These fungi typically use reactive oxygen species (ROS) to indiscriminately "loosen" wood cell walls at the outset of decay. Brown rot fungi avoid oxidative stress associated with this ROS step by delaying the expression/secretion of many carbohydrate-active enzymes, but there are exceptions, notably some side chain hemicellulases, implicated in loosening lignocellulose. In this study, we provide enzyme activity and secretomic evidence that these enzymes in the brown rot model Rhodonia placenta are more ROS tolerant than the white and soft rot isolates tested. For R. placenta, and perhaps all brown rot lineages, these ROS tolerance adaptions may have played a long-overshadowed role in enabling brown rot.

Coarse Woody Debris Decomposition Assessment Tool: Model validation and application.

Coarse woody debris (CWD) is a significant component of the forest biomass pool; hence a model is warranted to predict CWD decomposition and its role in forest carbon (C) and nutrient cycling under varying management and climatic conditions. A process-based model, CWDDAT (Coarse Woody Debris Decomposition Assessment Tool) was calibrated and validated using data from the FACE (Free Air Carbon Dioxide Enrichment) Wood Decomposition Experiment utilizing pine (Pinus taeda), aspen (Populous tremuloides) and birch (Betula papyrifera) on nine Experimental Forests (EF) covering a range of climate, hydrology, and soil conditions across the continental USA. The model predictions were evaluated against measured FACE log mass loss over 6 years. Four widely applied metrics of model performance demonstrated that the CWDDAT model can accurately predict CWD decomposition. The R2 (squared Pearson's correlation coefficient) between the simulation and measurement was 0.80 for the model calibration and 0.82 for the model validation (P<0.01). The predicted mean mass loss from all logs was 5.4% lower than the measured mass loss and 1.4% lower than the calculated loss. The model was also used to assess the decomposition of mixed pine-hardwood CWD produced by Hurricane Hugo in 1989 on the Santee Experimental Forest in South Carolina, USA. The simulation reflected rapid CWD decomposition of the forest in this subtropical setting. The predicted dissolved organic carbon (DOC) derived from the CWD decomposition and incorporated into the mineral soil averaged 1.01 g C m-2 y-1 over the 30 years. The main agents for CWD mass loss were fungi (72.0%) and termites (24.5%), the remainder was attributed to a mix of other wood decomposers. These findings demonstrate the applicability of CWDDAT for large-scale assessments of CWD dynamics, and fine-scale considerations regarding the fate of CWD carbon.

Retracted and Republished from: "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola"

Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed gene expression levels of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression was observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species­aspen, pine, and spruce­under various culture conditions. We found that F. pinicola is able to modify gene expression (transcription levels) across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This study provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.

Towards an Understanding of Oxidative Damage in an α-L-Arabinofuranosidase of Trichoderma reesei: a Molecular Dynamics Approach.

Trichoderma reesei is a "workhorse" fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on α-L-arabinofuranosidase, an enzyme important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render this enzyme inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of the protein when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized protein. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized protein, implying a less favorable reaction pathway. These results reveal the basis for loss of function in this carbohydrate active enzyme (CAZY) in the commercially relevant fungus T. reesei.

Coarse woody debris decomposition assessment tool: Model development and sensitivity analysis.

Coarse woody debris (CWD) is an important component in forests, hosting a variety of organisms that have critical roles in nutrient cycling and carbon (C) storage. We developed a process-based model using literature, field observations, and expert knowledge to assess woody debris decomposition in forests and the movement of wood C into the soil and atmosphere. The sensitivity analysis was conducted against the primary ecological drivers (wood properties and ambient conditions) used as model inputs. The analysis used eighty-nine climate datasets from North America, from tropical (14.2° N) to boreal (65.0° N) zones, with large ranges in annual mean temperature (26.5°C in tropical to -11.8°C in boreal), annual precipitation (6,143 to 181 mm), annual snowfall (0 to 612 kg m-2), and altitude (3 to 2,824 m above mean see level). The sensitivity analysis showed that CWD decomposition was strongly affected by climate, geographical location and altitude, which together regulate the activity of both microbial and invertebrate wood-decomposers. CWD decomposition rate increased with increments in temperature and precipitation, but decreased with increases in latitude and altitude. CWD decomposition was also sensitive to wood size, density, position (standing vs downed), and tree species. The sensitivity analysis showed that fungi are the most important decomposers of woody debris, accounting for over 50% mass loss in nearly all climatic zones in North America. The model includes invertebrate decomposers, focusing mostly on termites, which can have an important role in CWD decomposition in tropical and some subtropical regions. The role of termites in woody debris decomposition varied widely, between 0 and 40%, from temperate areas to tropical regions. Woody debris decomposition rates simulated for eighty-nine locations in North America were within the published range of woody debris decomposition rates for regions in northern hemisphere from 1.6° N to 68.3° N and in Australia.

Using aggregated field collection data and the novel r package fungarium to investigate fungal fire association.

Understanding which fungi exhibit certain ecological traits, such as habitat, host, or substrate associations, and knowing how these traits change across space and time can provide invaluable insight into the roles fungi play in their respective ecosystems. Archived sporocarp data, such as the collection and observation records accessible through the Mycology Collections Portal (MyCoPortal), are well suited for trait investigations, since these records circumvent the need for field work, are geographically and temporally diverse, and often have detailed and trait-relevant environmental metadata. However, there are inefficiencies and inadequacies in the MyCoPortal online interface that affect data set generation and trait searching, and many of the available records have outdated or misspelled taxon names as well as misspelled location names. Thus, we created the r package fungarium, which enables the efficient download of complete MyCoPortal data sets from within the R environment, enhances the identification of trait-relevant records, confirms or updates taxon names while also accounting for spelling errors, and fixes misspelled location names. Utilizing this package and MyCoPortal data, we demonstrated methods for analyzing taxonomic, geographic, and temporal patterns in ecological traits, using fire association as an example. We found that fire association, which was quantified via fire-associated enrichment factors (fire-associated records/total records), differed substantially between taxa, and these differences were qualitatively supported by existing literature, as hypothesized. Sampling bias within the MyCoPortal data and limitations of the burned acreage data set used (i.e., Monitoring Trends in Burn Severity) were identified as confounding factors in our geographic and temporal analyses, as evidenced by the unexpected lack of correlation between fire association and burned acreage on county and year bases. However, both confounding factors likely depend on the trait analyzed and external data set used. Overall, the fungarium package and associated methods presented here effectively enable the use of archived sporocarp data for future ecological trait studies.

Experimental nitrogen fertilisation globally accelerates, then slows decomposition of leaf litter.

Plant litter decomposition is a central process in the carbon (C) cycle and sensitive to ongoing anthropogenic nitrogen (N) fertilisation. Previous syntheses evaluating the effect of N fertilisation on litter decomposition relied largely on models that define a constant rate of mass loss throughout decomposition, which may mask hypothesised shifts in the effect of N fertilisation on litter decomposition dynamics. In this meta-analysis, we compared the performance of four empirical decomposition models and showed that N fertilisation consistently accelerates early-stage but slows late-stage decomposition when the model structure allows for flexibility in decomposition rates through time. Within a particular substrate, early-stage N-stimulation of decomposition was associated with reduced rates of late-stage decay. Because the products of early- vs. late-stage decomposition are stabilised in soils through distinct chemical and physical mechanisms, N-induced changes in the litter decomposition process may influence the formation and cycling of soil C, the largest terrestrial C pool.

High-efficiency methane capture by living fungi and dried fungal hyphae (necromass).

Fungi can hasten microbial degradation of hydrophobic compounds by enhancing capture and dissolution into biofilms. For methane (CH4 ) released from natural soils and agricultural systems, prokaryotes are ultimately responsible for oxidation and degradation; however, in many cases Henry's law of gas dissolution, not oxidation, is rate-limiting. Given that fungi can improve capture and bioremediation of other hydrophobic compounds (e.g., toluene), we tested fungi for CH4 capture. We used a batch system of CH4 -flooded vials to screen candidate fungi. We found 79% removal efficiency by Ganoderma lucidum relative to activated carbon. In a follow-up, we found comparable efficiency in other Ganoderma species (G. applanatum, G. meredithae). However, these efficiency gains by Ganoderma species could not be sustained when inoculated wood substrates were placed in "live" soils. Substrates colonized naturally, without preinoculations, performed similarly to those deployed with (native) test strains, likely because inoculated fungi were outcompeted and displaced by native colonizers. Instead of rescreening using more combative fungi, we tested an alternative way to present fungi with high single-strain efficiencies for filtration: in dried form as dead biomass (necromass). In dried biomass trials, dried G. lucidum biomass performed better than when testing living biomass, again with the highest strain-specific removal efficiencies (84% of activated carbon). These results demonstrate the potential for G. lucidum, commonly used in biomaterial production, in a variety of indoor and outdoor biofiltration scenarios. It also implies an overlooked, potentially large role for fungi and their soil necromass in capturing and reducing CH4 emissions from soils in nature.

Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms.

Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth's largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched ß-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.