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Abstract In the last two decades, studies on plant biomass-degrading fungi have remarkably increased to understand and reveal the underlying molecular mechanisms responsible for their life cycle and wood-decaying abilities. Most of the plant biomass-degrading fungi reported till date belong to basidiomycota or ascomycota phyla. Thus, very few studi...
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... (Mucoromycotina) and Mortierella elongata (Mortierellomycotina) encode higher number of genes distributed among the pathways except XBM and BpNp pathways. The selected microsporidia and cryptomycota fungi exhibited lower number of genes for all the selected pathways (Table 1). ...Context 2
... metadata analysis of fungal genomewide annotations especially CAZymes has been studied and reported Sista Kamesh- war and Qin 2017;Zhao et al. 2013). However, previous BpNp BSM CM E M GBM LM MCV MAA NM O X BM Gigaspora rosea 759 1 00 728 7 49 246 3 41 749 7 23 188 4 08 719 5 90 Rhizophagus diaphanus 626 1 06 533 5 48 185 2 66 488 5 56 143 3 30 478 4 29 Gonapodya prolifera 572 1 37 313 6 06 143 2 23 527 3 79 153 3 03 368 3 170 Catenaria anguillulae 308 2 1 1 51 296 8 7 9 9 2 35 248 7 7 1 74 245 1 55 Jimgerdemannia flammicorona 308 2 3 1 89 322 7 2 1 05 240 2 11 89 121 237 183 Caulochytrium protostelioides 300 1 24 88 498 9 1 1 83 194 1 93 53 350 1 67 89 Jimgerdemannia lactiflua 291 1 7 1 65 293 7 1 9 4 2 18 179 9 3 1 13 202 1 37 Coemansia reversa 271 4 3 1 45 350 1 32 195 2 60 265 9 3 2 48 216 1 54 Anaeromyces robustus 270 4 3 1 26 440 9 0 2 17 201 2 50 57 562 2 02 106 Thamnocephalis sphaerospora 268 1 4 1 57 241 5 5 8 0 1 96 198 9 3 1 37 236 162 Orpinomyces sp. 266 5 4 1 37 420 8 7 1 99 177 2 19 49 573 1 93 78 Endogone sp FLAS 59071 257 1 6 1 63 269 6 6 8 0 2 14 187 7 4 9 7 202 148 Syncephalis pseudoplumigaleata 257 1 5 1 31 212 7 3 6 7 1 72 166 6 9 1 03 206 1 06 Piromyces finnis 229 3 1 1 18 381 8 9 1 49 175 1 83 52 416 1 80 80 Piromyces sp. ...Context 3
... studied and reported Sista Kamesh- war and Qin 2017;Zhao et al. 2013). However, previous BpNp BSM CM E M GBM LM MCV MAA NM O X BM Gigaspora rosea 759 1 00 728 7 49 246 3 41 749 7 23 188 4 08 719 5 90 Rhizophagus diaphanus 626 1 06 533 5 48 185 2 66 488 5 56 143 3 30 478 4 29 Gonapodya prolifera 572 1 37 313 6 06 143 2 23 527 3 79 153 3 03 368 3 170 Catenaria anguillulae 308 2 1 1 51 296 8 7 9 9 2 35 248 7 7 1 74 245 1 55 Jimgerdemannia flammicorona 308 2 3 1 89 322 7 2 1 05 240 2 11 89 121 237 183 Caulochytrium protostelioides 300 1 24 88 498 9 1 1 83 194 1 93 53 350 1 67 89 Jimgerdemannia lactiflua 291 1 7 1 65 293 7 1 9 4 2 18 179 9 3 1 13 202 1 37 Coemansia reversa 271 4 3 1 45 350 1 32 195 2 60 265 9 3 2 48 216 1 54 Anaeromyces robustus 270 4 3 1 26 440 9 0 2 17 201 2 50 57 562 2 02 106 Thamnocephalis sphaerospora 268 1 4 1 57 241 5 5 8 0 1 96 198 9 3 1 37 236 162 Orpinomyces sp. 266 5 4 1 37 420 8 7 1 99 177 2 19 49 573 1 93 78 Endogone sp FLAS 59071 257 1 6 1 63 269 6 6 8 0 2 14 187 7 4 9 7 202 148 Syncephalis pseudoplumigaleata 257 1 5 1 31 212 7 3 6 7 1 72 166 6 9 1 03 206 1 06 Piromyces finnis 229 3 1 1 18 381 8 9 1 49 175 1 83 52 416 1 80 80 Piromyces sp. E2 224 4 1 1 21 418 7 8 1 96 185 2 24 58 511 1 89 91 Blyttiomyces helicus 215 8 111 2 77 63 78 200 1 41 107 1 27 157 1 17 Piptocephalis cylindrospora 162 1 4 7 8 1 62 47 46 113 1 22 41 62 123 7 ...Citations
... Although members of the Basidiomycota and Ascomycota phyla, especially those inhabiting soil and wood, are primarily known for their capacity to produce ligninolytic enzymes, it has been demonstrated that representatives of the phylum Mucoromycota can also possess this capability [47][48][49]. The obtained results suggest that fungal communities on investigated objects, reflected in culturable mycobiota, are mostly characterized by taxa capable of producing ligninolytic enzymes. ...
... This activity was not demonstrated at all for fungi of genera Mucor, Scytalidium, and Trichoderma, although the literature data suggest that species from these genera are capable of ligninolytic enzyme production [50][51][52]. Furthermore, Lunasporangiospora selenospora (formerly Mortierella selenospora) showed no ligninolytic activity, even though it was previously demonstrated that fungi of this genus can be good laccase producers [49]. Additionally, whole-genome sequencing of M. elongata demonstrated the presence of laccase genes [48]. ...
Two ancient wooden vessels, specifically a monoxyle (1st century BCE to 1st century CE) and shipwreck (15th to 17th century CE), were excavated in a well-preserved state east of the confluence of the old Mlava and the Danube rivers (Serbia). The vessels were found in the ground that used to be river sediment and were temporarily stored within the semi-underground exhibition space of Mammoth Park. As part of the pre-conservation investigations, the primary aim of the research presented was to characterize the culturable mycobiomes of two excavated wooden artifacts so that appropriate conservation procedures for alleviating post-excavation fungal infestation could be formulated. Utilizing culture-based methods, a total of 32 fungi from 15 genera were identified, mainly Ascomycota and to a lesser extent Mucoromycota sensu stricto. Soft-rot Ascomycota of genus Penicillium, followed by Aspergillus and Cephalotrichum species, were the most diverse of the isolated fungi. Out of a total of 38 isolates, screened on 7 biodegradation plate assays, 32 (84.21%) demonstrated at least one degradative property. Penicillium solitum had the highest deterioration potential, with a positive reaction in 5 separate plate assays. The obtained results further broaden the limited knowledge on the peculiarities of post-excavation soft-rot decay of archaeological wood and indicate the biochemical mechanisms at the root of post-excavation fungal deterioration.
... Furthermore, in our study, the abundance of Chytridiomycota increased while that of Morteriellomycota decreased along the rural-urban gradient. Most Chytridiomycota and Ascomycota are saprotrophic fungi living on decaying plant material [51]. The higher abundance of Chytridiomycota in urban forests than in rural forests may therefore be due to the higher amount of soil organic matter recorded in urban forests than in rural forests (Table 2; +21%). ...
The functioning of forest ecosystems depends on the taxonomic and ecological diversity of soil fungi. Urbanization is increasing worldwide and is regarded as a key driver of environmental change altering local species assemblages in urban forest. We investigated whether the degree of urbanization and local forest characteristics affect the soil fungal community in 20 beech forests located along a rural–urban gradient in the city of Basel and its suburbs (Switzerland). We analyzed their soil fungal communities by DNA metabarcoding of the rDNA ITS2 region and related these data to local forest vegetation characteristics and soil properties. The number of fungal OTUs in the 20 forests examined ranged from 170 to 303. Richness, diversity and evenness of fungal communities were all significantly affected by the degree of urbanization, but in different ways. Soil fungal richness was highest in forests in areas with a low degree of urbanization and lowest in forests in rural areas. In contrast, the fungal community diversity increased with the increasing degree of urbanization. Different fungal phyla and fungal guilds showed distinct patterns in their relative abundance along the rural–urban gradient. The degree of urbanization reduced the relative abundance of symbiotrophic fungi, but increased that of saprotrophic and pathotrophic fungi. Our results show that urbanization changes soil fungal community, which in turn can lead to alterations in forest ecosystems.
... The composition of soil fungal community found in our study, with Basiodiomycota as the dominant fungal phyla, followed by Ascomycota and Morteriellomycota, is characteristic for the soil fungal community in beech forests [55,59,66,67]. Consistent with our second hypothesis, we showed that the different fungal phyla were differently affected by the degree of urbanization. ...
The functioning of forest ecosystems depends on the taxonomic and ecological diversity of soil fungi. Urbanization is increasing worldwide and is regarded a major driver of environmental change altering local species assemblages in urban forest. We investigated whether the degree of urbanization and local forest characteristics affect the soil fungal community in 20 beech forests located along a rural–urban gradient in the city of Basel and its suburbs (Switzerland). We analyzed their soil fungal communities by DNA metabarcoding of the rDNA ITS2 region and related these data to local forest vegetation characteristics and soil properties. The number of fungal OTUs in the 20 forests examined ranged from 170 to 303. Richness, diversity and evenness of fungal OTUs were all significantly affected by the degree of urbanization, but in different ways. OTU richness was highest in forests in areas with a low degree of urbanization and lowest in forests in rural areas. In contrast, the diversity of OTUs increased with increasing degree of urbanization. Different fungal phyla and fungal guilds showed distinct patterns in their relative abundance along the rural-urban gradient. The degree of urbanization reduced the relative abundance of symbiotrophic fungi, but increased that of saprotrophic and pathotrophic fungi. Our results show that urbanization alters soil fungal community, which in turn can lead to changes in forest ecosystems.
... ; https://doi.org/10.1101/2023.08.30.555587 doi: bioRxiv preprint to be effectors that may aid infection ( Figure 1D). We additionally identified carbohydrate-active enzymes (CAZymes), a group of proteins that catalytically alter or break glycosidic bonds that fungal plant pathogens use to degrade carbohydrates such as components of plant cell walls (92). We identified 519 to 534 CAZymes ( Figure 1D). ...
Genome organization in eukaryotes exhibits non-random patterns tied to transcription, replication, and chromatin. However, the driving forces across these processes, and their impacts on genome evolution remain unclear. To address this, we analyzed sequence data from 86 Magnaporthe oryzae isolates, a globally important plant pathogenic fungus, alongside new reference genomes, to investigate DNA sequence variation and the epigenome. Histone modification profiles were obtained through genome-wide chromatin immunoprecipitation-sequencing of the four new reference strains, which revealed that repressive histone marks (H3K27me3, H3K9me3) were associated with SNP and INDEL frequency. Densely grouped SNPs were found to reside in heterochromatin, often outside transposable elements, highlighting the link between heterochromatin and DNA variation. Even when controlling for selection, silent SNP frequency/kb was higher in H3K27me3-associated genes. Effector genes, key to pathogenicity, also displayed this trend. Comparing the reference strains, euchromatic regions were often syntenic, while heterochromatic regions trended towards non-syntenic. Heterochromatin emerged as a major factor associated with diverse DNA variations in M. oryzae populations, even when accounting for selective pressure. This underscores heterochromatin's pivotal role in shaping genetic diversity in these mainly asexually reproducing fungi.
... whose relative abundances were by 33% and 8% higher in brown-than white-rot sets in the deciduous and coniferous forest stands, respectively (Table 1). All of the abovementioned fungal phyla ubiquitously exist in soil and are highly related to the decomposition of lignocellulosic substances [44,[47][48][49]. In general, basidiomycetous wood-decaying fungi (especially for white-rot decay) owe more powerful abilities in decomposing aromatic lignin polymers compared to ascomycetous fungi [47,48,50]. ...
... All of the abovementioned fungal phyla ubiquitously exist in soil and are highly related to the decomposition of lignocellulosic substances [44,[47][48][49]. In general, basidiomycetous wood-decaying fungi (especially for white-rot decay) owe more powerful abilities in decomposing aromatic lignin polymers compared to ascomycetous fungi [47,48,50]. Under oxic condition, for instance, Basidiomycota isolates may prefer to degrade lignin via ligninolytic enzymes, whereas Ascomycota members are more likely to produce cellulosedegrading extracellular enzymes [51]. ...
... Glomeromycota fungi may have low cellulolytic and ligninolytic potentials due to a lack of genes encoding for cellulolytic glycoside hydrolase families and ligninolytic auxiliary activity enzymes. However, they can exhibit a large number of genes encoding for Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic and regulatory pathways, including amino acid metabolism, carbohydrate metabolism and lipid metabolism [48]. Their existence may not cause much consumption of lignin and cellulose but definitely reduce certain NS components (e.g., lipids and amino acids). ...
Although the bioconversion of lignocellulosic residues is essential for nutrient storage in forest floors, little is known about the mechanisms behind wood decay and its interactions with site-specific belowground microbial community composition and chemical properties. This study examined the components of white-rot vs. brown-rot woody debris, closely contacted soil chemical properties and microbial community composition using high-throughput Illumina MiSeq sequencing in coniferous and deciduous temperate forests. The lignin concentrations were higher in the brown-rot than in the white-rot woody debris of the coniferous forest. However, lower cellulose concentrations were observed in the brown-rot sets than in the white-rot sets of both coniferous and deciduous forest stands. Furthermore, the woody debris had higher concentrations of nonstructural compounds and ash in the brown-rot than in the white-rot sets of the coniferous and deciduous forests, respectively. Surprisingly, nearly 90% of the variation in the woody debris components was explained by the belowground fungal and bacterial phylum-level compositions. Of these major phyla, Basidiomycota was closely related to the lignin concentration and accounted for 26.62% of the variation in woody debris components, while Ascomycota was related to the hemicellulose concentration and accounted for 17.7% of the variance in the woody debris components. Furthermore, soil total carbon, available phosphorus, and available potassium were 131%, 138%, and 91% higher in the brown-rot than white-rot sets of the coniferous (but not deciduous) forest stand. In addition, Basidiomycota fungi presented an oligotrophic life strategy and were significantly negatively correlated with the soil total carbon, total nitrogen, alkali-hydrolysable nitrogen, and available phosphorus contents. In contrast, Ascomycota fungi were characterized by a copiotrophic strategy and were positively correlated with the contents of soil total carbon, total nitrogen, and total phosphorus. These findings indicate that wood decay processes are strongly determined by site-specific microbial community structure and nutrient status in temperate forests.
... The laccase activity was experimentally demonstrated for this species [35]. All above-mentioned AAs (AA3, AA5 and AA6) were also present in Mucoromycota, as previously shown by Kameshwar and Qin [36], and the expansion of AA5 was observed in arbuscular mycorrhizal fungi Glomeromycotina. However, Glomeromycotina are considered as weak degraders [37]. ...
Early-diverging fungi (EDF) are ubiquitous and versatile. Their diversity is reflected in their genome sizes and complexity. For instance, multiple protein families have been reported to expand or disappear either in particular genomes or even whole lineages. The most commonly mentioned are CAZymes (carbohydrate-active enzymes), peptidases and transporters that serve multiple biological roles connected to, e.g., metabolism and nutrients intake. In order to study the link between ecology and its genomic underpinnings in a more comprehensive manner, we carried out a systematic in silico survey of protein family expansions and losses among EDF with diverse lifestyles. We found that 86 protein families are represented differently according to EDF ecological features (assessed by median count differences). Among these there are 19 families of proteases, 43 CAZymes and 24 transporters. Some of these protein families have been recognized before as serine and metallopeptidases, cellulases and other nutrition-related enzymes. Other clearly pronounced differences refer to cell wall remodelling and glycosylation. We hypothesize that these protein families altogether define the preliminary fungal adaptasome. However, our findings need experimental validation. Many of the protein families have never been characterized in fungi and are discussed in the light of fungal ecology for the first time.
... We blasted this database against our two sanchytrid proteomes and other two representatives of Blastocladiomycota and four Chytridiomycota. We then screened for canonical cellulose-, hemicellulose-, pectin-and chitin-degrading enzymes identified in Fungi from the previous studies 13,131,132 . The identified hits were blasted back to both the NCBI non-redundant protein sequence database and the CAZy database (cazy.org) to create a dataset for phylogenetic reconstruction for each enzyme. ...
Compared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living flagellated stages (zoospores) remain poorly known and their phylogenetic position is often unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and Sanchytrium tribonematis , showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchytrids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages.
... A significant portion (35-50%) of upregulated genes were annotated as CBM67s in the CAZy database [44]. CBM67 are L-rhamnose binding modules, which are reported to be involved in pectin degradation [17,74]. Apart from CBM67, there were a number of other pectinolytic enzymes (e.g., GH78, PL4) associated with these GBDPs, which were upregulated in the two species (Supplementary Table S6). ...
... There was one downstream multicopper oxidase gene with increased abundance in the mycelium only of A. cepistipes and not in A. ostoyae. The iron permease system along with iron reductases and MCOs is specifically seen upregulated in brown-rot wood decay [56,67,74,[76][77][78]. ...
... Several aspects of the gene expression patterns in our assays are unusual for whiterot fungi. These include the lack of an early burst of LDE encoding gene expression as is typical for white-rot fungi and the high expression of some genes (e.g., iron uptake systems, oxoglutarate/iron-dependent dioxygenases) that have been reported from brown rot fungi [74,[76][77][78]. Previous studies questioned the typical white-rot nature of Armillaria [20,22,23,96]. ...
Wood-decaying Basidiomycetes are among the most efficient degraders of plant cell walls, making them key players in forest ecosystems, global carbon cycle, and in bio-based industries. Recent insights from -omics data revealed a high functional diversity of wood-decay strategies, especially among the traditional white-rot and brown-rot dichotomy. We examined the mechanistic bases of wood-decay in the conifer-specialists Armillaria ostoyae and Armillaria cepistipes using transcriptomic and proteomic approaches. Armillaria spp. (Fungi, Basidiomycota) include devastating pathogens of temperate forests and saprotrophs that decay wood. They have been discussed as white-rot species, though their response to wood deviates from typical white-rotters. While we observed an upregulation of a diverse suite of plant cell wall degrading enzymes, unlike white-rotters, they possess and express an atypical wood-decay repertoire in which pectinases and expansins are enriched, whereas lignin-decaying enzymes (LDEs) are generally downregulated. This combination of wood decay genes resembles the soft-rot of Ascomycota and appears widespread among Basidiomycota that produce a superficial white rot-like decay. These observations are consistent with ancestral soft-rot decay machinery conserved across asco- and Basidiomycota, a gain of efficient lignin-degrading ability in white-rot fungi and repeated, complete, or partial losses of LDE encoding gene repertoires in brown- and secondarily soft-rot fungi.
... Genome mining for genes coding enzymes known to be involved in lignin degradation (i.e., genes encoding AA enzymes) is another method to address whether a particular species may be able to break down lignin and how it may do so. This has extensively been applied to basidiomycetes (see for example Eastwood et al., 2011;Floudas et al., 2012;Nagy et al., 2017) and even to early diverging fungi (Kameshwar & Qin, 2019). Yet, there is very little data available for ascomycetes, especially regarding their coding capacity for AA enzymes. ...
... We blasted this database against our two sanchytrid proteomes and other two representatives of Blastocladiomycota and four Chytridiomycota. We then screened for canonical cellulose-, hemicellulose-, pectin-and chitin-degrading enzymes identified in Fungi from the previous studies 13,131,132 . The identified hits were blasted back to both the NCBI non-redundant protein sequence database and the CAZy database (cazy.org) to create a dataset for phylogenetic reconstruction for each enzyme. ...
Compared to well-known multicellular fungi and unicellular yeast, unicellular fungi with zoosporic, free-living flagellated stages remain poorly known and their phylogenetic position is often unresolved. Recently, 18S+28S rRNA gene molecular phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and record-long simplified kinetosomes, Amoeboradix gromovi and Sanchytrium tribonematis , showed that they formed a monophyletic group without affinity with any known fungal clade. To assess their phylogenetic position and unique trait evolution, we sequenced single-cell genomes for both species. Phylogenomic analyses using 264 protein markers and a comprehensive taxon sampling retrieved and almost fully-resolved fungal tree with these species forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Chytridiomycota branched as sister to all other fungi, and the zoosporic fungus Olpidium bornovanus as sister to non-flagellated fungi. Comparative genomic analyses across Holomycota revealed an atypically reduced metabolic repertoire for sanchytrids given their placement in the tree. We infer four independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. The highly reduced sanchytrid flagellar machinery, notably their long kinetosome, might have been retained to support a putative light-sensing lipid organelle. Together with their phylogenetic position, these unique traits justify the erection of the novel phylum Sanchytriomycota. Our results also show that most of the hyphal morphogenesis gene repertoire of multicellular Fungi had already evolved in early holomycotan lineages.
