1. |
- Björnerås, Caroline, et al.
(författare)
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High sulfate concentration enhances iron mobilization from organic soil to water
- 2019
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Ingår i: Biogeochemistry. - : Springer Science and Business Media LLC. - 0168-2563 .- 1573-515X. ; 144:3, s. 245-259
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Tidskriftsartikel (refereegranskat)abstract
- Widespread increases in iron (Fe) concentrations are contributing to ongoing browning of northern freshwaters, but the driver/s behind the trends are not known. Fe mobilization in soils is known to be controlled by redox conditions, pH, and DOC availability for complexation. Moreover, high sulfate concentrations have been suggested to constrain Fe in transition from soil to water, and declining sulfate deposition to have the opposite effect. We studied the effect of these Fe mobilization barriers in a microcosm experiment, applying high (peak S deposition) and low (present day) sulfate treatments and oxic versus anoxic conditions to boreal (O horizon) soil slurries. We hypothesized that anoxic conditions would favor Fe release. On the contrary we expected high sulfate concentrations to suppress Fe mobility, through FeS formation or by lowering pH and thereby DOC concentrations. Anoxia had positive effects on both Fe and DOC concentrations in solution. Contrasting with our hypothesis, Fe concentrations were enhanced at high sulfate concentrations, i.e. increasing acidity in high sulfate treatments appeared to promote Fe mobilization. Establishment of the basidiomycete fungus Jaapia ochroleuca in the oxic treatments 44 days into the experiment had a major impact on Fe mobilization by increasing total Fe concentrations in solution. Thus, anoxia and acidity, along with fungi mediated mobilization, were important in controlling Fe release from soil to the aqueous phase. While Fe is often assumed to precipitate as Fe(oxy)hydroxides in the transition from anoxic to oxic water in the riparian zone, Fe from anoxic treatments remained in solution after introduction of oxygen. Our results do not support reduced atmospheric S deposition as a driver behind increasing Fe concentrations in boreal freshwaters, but confirm the importance of reducing conditions—which may be enhanced by higher soil temperature and moisture—for mobilization of Fe across the terrestrial-aquatic interphase.
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2. |
- Floudas, Dimitrios
(författare)
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Evolution of lignin decomposition systems in fungi
- 2021
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Ingår i: Advances in Botanical Research. - : Elsevier. - 0065-2296. ; 99, s. 37-76
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Bokkapitel (refereegranskat)abstract
- Lignin represents the second most abundant biopolymer of the plant cell wall. Among microorganisms, fungi are the most efficient lignin decomposers. The discovery of ligninolysis by fungi could have altered the ancient carbon cycle at the global scale and it is still one of the processes that determine carbon sequestration and soil formation. Understanding the evolution of ligninolytic systems represents a great challenge because lignin decomposition relies on complex gene networks, for which we have only fragmented information. Moreover, not all fungi can break down lignin and among ligninolytic fungi, there is enormous variation in ligninolytic efficiency, which has not been documented extensively. Genomic sequences offer an extraordinary opportunity to understand evolutionary processes. Here, we present the contribution of fungal comparative genomics to the evolution of ligninolytic systems in fungi and we conclude with a series of questions that remain to be answered.
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3. |
- Floudas, Dimitrios, et al.
(författare)
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Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii
- 2015
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845. ; 76, s. 78-92
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Tidskriftsartikel (refereegranskat)abstract
- Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited. (C) 2015 Elsevier Inc. All rights reserved.
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4. |
- Floudas, Dimitrios, et al.
(författare)
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Revisiting the taxonomy of Phanerochaete (Polyporales, Basidiomycota) using a four gene dataset and extensive ITS sampling.
- 2015
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Ingår i: Fungal Biology. - : Elsevier BV. - 1878-6146. ; 119:8, s. 679-719
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Tidskriftsartikel (refereegranskat)abstract
- We amplified RPB1, RPB2, and the ITS and LSU ribosomal genes from species mostly in the phlebioid clade, focusing heavily in phanerochaetoid taxa. We performed Maximum Likelihood and Bayesian analyses for different combinations of datasets. Our results provide a strongly supported phylogenetic picture of the phlebioid clade, representing 89 species in the four genes analyses, of which 49 represent phanerochaetoid taxa. Phanerochaete sensu lato is polyphyletic and distributed across nine lineages in the phlebioid clade. Six of these lineages are associated to already described genera, while we describe the new genus Phaeophlebiopsis to accommodate Phlebiopsis-like species in one of the remaining lineages. We also propose three taxonomic transfers and describe nine new species, with four of those species currently placed in Phanerochaete sanguinea or Phanerochaete velutina. Finally, the placement of Leptoporus mollis along with other potential brown-rot species in the phlebioid clade suggests that, in addition to the Antrodia clade, brown-rot fungi may have evolved more than once in Polyporales.
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5. |
- Floudas, Dimitrios, et al.
(författare)
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Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi
- 2020
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 14:8, s. 2046-2059
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Tidskriftsartikel (refereegranskat)abstract
- Litter decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.
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6. |
- Floudas, Dimitrios, et al.
(författare)
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X-ray scattering reveals two mechanisms of cellulose microfibril degradation by filamentous fungi
- 2022
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 88:17
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Tidskriftsartikel (refereegranskat)abstract
- Mushroom-forming fungi (Agaricomycetes) employ enzymatic and nonenzymatic cellulose degradation mechanisms, the latter presumably relying on Fenton-generated radicals. The effects of the two mechanisms on the cellulose microfibrils structure remain poorly understood. We examined cellulose degradation caused by litter decomposers and wood decomposers, including brown-rot and white-rot fungi and one fungus with uncertain wood decay type, by combining small- and wide-angle X-ray scattering. We also examined the effects of commercial enzymes and Fenton-generated radicals on cellulose using the same method. We detected two main degradation or modification mechanisms. The first characterized the mechanism used by most fungi and resembled enzymatic cellulose degradation, causing simultaneous microfibril thinning and decreased crystalline cellulose. The second mechanism was detected in one brown-rot fungus and one litter decomposer and was characterized by patchy amorphogenesis of crystalline cellulose without substantial thinning of the fibers. This pattern did not resemble the effect of Fenton-generated radicals, suggesting a more complex mechanism is involved in the destruction of cellulose crystallinity by fungi. Furthermore, our results showed a mismatch between decay classifications and cellulose degradation patterns and that even within litter decomposers two degradation mechanisms were found, suggesting higher functional diversity under current ecological classifications of fungi.IMPORTANCE Cellulose degradation by fungi plays a fundamental role in terrestrial carbon cycling, but the mechanisms by which fungi cope with the crystallinity of cellulose are not fully understood. We used X-ray scattering to analyze how fungi, a commercial enzyme mix, and a Fenton reaction-generated radical alter the crystalline structure of cellulose. Our data revealed two mechanisms involved in crystalline cellulose degradation by fungi: one that results in the thinning of the cellulose fibers, resembling the enzymatic degradation of cellulose, and one that involves amorphogenesis of crystalline cellulose by yet-unknown pathways, resulting in a patchy-like degradation pattern. These results pave the way to a deeper understanding of cellulose degradation and the development of novel ways to utilize crystalline cellulose.
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7. |
- Gentile, Luigi, et al.
(författare)
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Fungal decomposition and transformation of molecular and colloidal fractions of dissolved organic matter extracted from boreal forest soil
- 2024
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Ingår i: Soil Biology and Biochemistry. - 0038-0717. ; 195
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Tidskriftsartikel (refereegranskat)abstract
- Dissolved organic matter (DOM) plays a central role in soil carbon (C) dynamics, serving as both a substrate for microbial decomposers and a source of material stabilised via physical protection in molecular aggregates and associations with mineral particles. It is well established that soil microorganisms play a key role in mineral-associated C aggregates; however, their impacts on molecular aggregates is not clearly understood. Here, we examined the ability of an ectomycorrhizal fungus (Paxillus involutus) and a saprotrophic fungus (a strain of Gloeophyllum), two major functional groups of fungal decomposers in forest ecosystems, to decompose and process the molecular and colloidal size fractions of DOM. DOM was extracted by water from boreal forest soil, and the chemical composition and colloidal properties were followed over 11 days using nuclear magnetic resonance (NMR) spectroscopy and small-angle light and X-ray scattering techniques. Both fungi decompose various organic compounds into their molecular fractions in the presence of an energy source (i.e. glucose). The decomposition rate was significantly higher for Gloeophyllum than for P. involutus. When glucose was depleted, Gloeophyllum continued to decompose more complex carbohydrates, whereas the decomposition activity of P. involutus almost stopped. A large proportion of the C in the DOM was found in organic colloids. At later stages, Gloeophyllum but not P. involutus, significantly affected the colloids by promoting the formation of larger aggregates. Thus, saprotrophic fungi activity can significantly influence the colloidal properties of DOM. Our results support the view that ectomycorrhizal fungi decompose some of the soil organic C however, their overall capacity for DOM decomposition and transformation is significantly lower than that of saprotrophic fungi.
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8. |
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9. |
- Goidea, Ana, et al.
(författare)
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Transcalar Design : An Approach to Biodesign in the Built Environment
- 2022
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Ingår i: Infrastructures. - : MDPI AG. - 2412-3811. ; 7:4
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Tidskriftsartikel (refereegranskat)abstract
- Biodesign holds the potential for radically increasing the sustainability of the built environment and our material culture but comes with new challenges. One of these is the bridging of the vast differences of scale between microbiological processes and architecture. We propose that a transcalar design approach, which weaves together nonlinear dependencies using computational design tools and design methodologies through the biological generation of architectural components, is a way towards successful design implementations. Such design processes were explored in a laboratory-based fabrication and study of a column element. This column, named Protomycokion, serves to illustrate how design methodologies, particularly through the use of a demonstrator artefact, can serve to navigate the multiple scales, disciplines, and experiments that are necessary to engage the complexities of biodesign. Transcalar design processes embrace the adaptability, variability and inter-dependence of biological organisms and show possible gains with regard to material sustainability and increased performativity.
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10. |
- Justo, Alfredo, et al.
(författare)
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A revised family-level classification of the Polyporales (Basidiomycota)
- 2017
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Ingår i: Fungal Biology. - : Elsevier BV. - 1878-6146. ; 121:9, s. 798-824
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Tidskriftsartikel (refereegranskat)abstract
- Polyporales is strongly supported as a clade of Agaricomycetes, but the lack of a consensus higher-level classification within the group is a barrier to further taxonomic revision. We amplified nrLSU, nrITS, and rpb1 genes across the Polyporales, with a special focus on the latter. We combined the new sequences with molecular data generated during the PolyPEET project and performed Maximum Likelihood and Bayesian phylogenetic analyses. Analyses of our final 3-gene dataset (292 Polyporales taxa) provide a phylogenetic overview of the order that we translate here into a formal family-level classification. Eighteen clades are assigned a family name, including three families described as new (Cerrenaceae fam. nov., Gelatoporiaceae fam. nov., Panaceae fam. nov.) and fifteen others (Dacryobolaceae, Fomitopsidaceae, Grifolaceae, Hyphodermataceae, Incrustoporiaceae, Irpicaceae, Ischnodermataceae, Laetiporaceae, Meripilaceae, Meruliaceae, Phanerochaetaceae, Podoscyphaceae, Polyporaceae, Sparassidaceae, Steccherinaceae). Three clades are given informal names (/hypochnicium,/climacocystis and/fibroporia + amyloporia). Four taxa (Candelabrochete africana, Mycoleptodonoides vassiljevae, Auriporia aurea, and Tyromyces merulinus) cannot be assigned to a family within the Polyporales. The classification proposed here provides a framework for further taxonomic revision and will facilitate communication among applied and basic scientists. A survey of morphological, anatomical, physiological, and genetic traits confirms the plasticity of characters previously emphasized in taxonomy of Polyporales.
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11. |
- Kohler, Annegret, et al.
(författare)
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Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 176-410
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Tidskriftsartikel (refereegranskat)abstract
- To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
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12. |
- Nagy, László G, et al.
(författare)
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Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities.
- 2015
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 33:4, s. 959-970
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Tidskriftsartikel (refereegranskat)abstract
- Evolution of lignocellulose decomposition was one of the most ecologically important innovations in fungi. White rot fungi in the Agaricomycetes (mushrooms and relatives) are the most effective microorganisms in degrading both cellulose and lignin components of woody plant cell walls (PCW). However, the precise evolutionary origins of lignocellulose decomposition are poorly understood, largely because certain early-diverging clades of Agaricomycetes and its sister group, the Dacrymycetes, have yet to be sampled, or have been undersampled, in comparative genomic studies. Here, we present new genome sequences of 10 saprotrophic fungi, including members of the Dacrymycetes and early-diverging clades of Agaricomycetes (Cantharellales, Sebacinales, Auriculariales, and Trechisporales), which we use to refine the origins and evolutionary history of the enzymatic toolkit of lignocellulose decomposition. We reconstructed the origin of ligninolytic enzymes, focusing on class II peroxidases (AA2), as well as enzymes that attack crystalline cellulose. Despite previous reports of white rot appearing as early as the Dacrymycetes, our results suggest that white rot fungi evolved later in the Agaricomycetes, with the first class II peroxidases reconstructed in the ancestor of the Auriculariales and residual Agaricomycetes. The exemplars of the most ancient clades of Agaricomycetes that we sampled all lack class II peroxidases, and are thus concluded to use a combination of plesiomorphic and derived PCW degrading enzymes that predate the evolution of white rot.
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13. |
- Nicolás, César, et al.
(författare)
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The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen
- 2018
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370.
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Tidskriftsartikel (refereegranskat)abstract
- Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.
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14. |
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15. |
- Tunlid, Anders, et al.
(författare)
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Decomposition of soil organic matter by ectomycorrhizal fungi : Mechanisms and consequences for organic nitrogen uptake and soil carbon stabilization
- 2022
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Ingår i: Frontiers in Forests and Global Change. - : Frontiers Media SA. - 2624-893X. ; 5
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Forskningsöversikt (refereegranskat)abstract
- A major fraction of nitrogen (N) in boreal forest soils is found in organic forms associated with soil organic matter (SOM) and mineral particles. The capacity of ectomycorrhizal (ECM) fungal symbionts to access this N is debated, considering that these fungi have lost many of the genes for decomposing organic matter that were present in their saprotrophic ancestors. To gain a molecular-level understanding of the N-mining processes in ECM fungi, we developed an experimental approach where the processes of decomposition were studied in parallel with the changes in the structure and properties of the organic matter. We showed that ECM fungi have significant capacities to assimilate organic N associated with SOM and mineral surfaces. The decomposition mechanisms differ between species, reflecting the lignocellulose decomposition mechanisms found in their saprotrophic ancestors. During N-mining, the ECM fungi processed the SOM to a material with increased adsorptive properties to iron oxide mineral particles. Two pathways contributed to these changes: Extracellular modifications of the SOM and secretion of mineral surface reactive metabolites. Some of these metabolites have iron(III)-reducing activities and can participate in extracellular Fenton reactions and redox reactions at iron oxide mineral surfaces. We conclude that the traditional framework for understanding organic N acquisition by ECM fungi from recalcitrant SOM must be extended to a framework that includes how those decomposition activities affect the stabilization and reactivity of mineral-associated SOM. The activity through these complex networks of reactions is decisive for the overall effect of ECM fungal decomposition on nutrients and C-cycling in forest ecosystems.
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16. |
- Tunlid, Anders, et al.
(författare)
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Soil organic matter decomposition mechanisms in ectomycorrhizal fungi
- 2016
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Ingår i: Molecular Mycorrhizal Symbiosis. - Hoboken, NJ, USA : John Wiley & Sons, Inc.. - 9781118951415 - 9781118951446 ; , s. 257-275
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Bokkapitel (refereegranskat)abstract
- In boreal forests, ectomycorrhizal (ECM) fungi are found in soil layers containing decomposed litter and humus-rich soil organic matter (SOM). This chapter summarizes the present understanding of the mechanisms for oxidative decomposition of SOM and the hydrolysis and mobilization of organic N and P sources by ECM fungi. It discusses how these processes may influence the formation and stability of SOM, and the interactions with saprotrophic microorganisms in forest ecosystems. The chapter gives a brief introduction to litter decomposition mechanisms in saprotrophic fungi. To investigate experimentally the capacity of ECM fungi to decompose humic-rich SOM and the mechanisms underlying this decomposition, a series of experiments have been conducted using Paxillus involutus as a "model" species. ECM fungi have evolved from diverse nutritional backgrounds, including litter decomposers and WR and BR wood decayers. During these transitions, ECM lineages lost many genes related to saprotrophy. There is evidence that some ECM employ the Fenton reaction during SOM decomposition.
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17. |
- Wu, Sheng Hua, et al.
(författare)
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Two new species of Phanerochaete (Basidiomycota) and redescription of P. robusta
- 2018
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Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 17:4, s. 425-435
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Tidskriftsartikel (refereegranskat)abstract
- In the current study, the new species Phanerochaete bambucicola and P. incarnata, from subtropical Taiwan are presented, while P. robusta is redescribed. We amplified the 5.8 s and LSU ribosomal genes along with RPB1. We generated an ITS dataset and a concatenated 5.8 s + nLSU + RPB1 dataset, which we analyzed using Maximum Parsimony and Bayesian methods. Our results suggest that the two new species belong in Phanerochaete s.s. P. bambucicola was collected on dead bamboo culm, characterized by the loose subiculum, the presence of leptocystidia, and the short lateral branches occasionally seen on the subicular hyphae. P. incarnata is characterized by the pink hymenial surface, and the presence of leptocystidia, which are usually covered with yellowish resinous material. The presence of enclosed, irregularly swollen, leptocystidia with oil drops is reported for P. robusta.
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18. |
- Zanne, Amy E, et al.
(författare)
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Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.
- 2020
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Ingår i: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433
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Tidskriftsartikel (refereegranskat)abstract
- Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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