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- Barbi, Florian
(author)
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Datamining and functional environmental genomics reassess the phylogenetics and functional diversity of fungal monosaccharide transporters
- 2021
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In: Applied Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0175-7598 .- 1432-0614. ; 105, s. 647-660
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Journal article (peer-reviewed)abstract
- Sugar transporters are essential components of carbon metabolism and have been extensively studied to control sugar uptake by yeasts and filamentous fungi used in fermentation processes. Based on published information on characterized fungal sugar porters, we show that this protein family encompasses phylogenetically distinct clades. While several clades encompass transporters that seemingly specialized on specific "sugar-related" molecules (e.g., myo-inositol, charged sugar analogs), others include mostly either mono- or di/oligosaccharide low-specificity transporters. To address the issue of substrate specificity of sugar transporters, that protein primary sequences do not fully reveal, we screened "multi-species" soil eukaryotic cDNA libraries for mannose transporters, a sugar that had never been used to select transporters. We obtained 19 environmental transporters, mostly from Basidiomycota and Ascomycota. Among them, one belonged to the unusual "Fucose H+ Symporter" family, which is only known in Fungi for a rhamnose transporter in Aspergillus niger. Functional analysis of the 19 transporters by expression in yeast and for two of them in Xenopus laevis oocytes for electrophysiological measurements indicated that most of them showed a preference for d-mannose over other tested d-C6 (glucose, fructose, galactose) or d-C5 (xylose) sugars. For the several glucose and fructose-negative transporters, growth of the corresponding recombinant yeast strains was prevented on mannose in the presence of one of these sugars that may act by competition for the binding site. Our results highlight the potential of environmental genomics to figure out the functional diversity of key fungal protein families and that can be explored in a context of biotechnology.
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| 2. |
- Barbi, Florian, et al.
(author)
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Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers
- 2020
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In: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 22, s. 1089-1103
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Journal article (peer-reviewed)abstract
- Microbial communities interplay with their environment through their functional traits that can be a response or an effect on the environment. Here, we explore how a functional trait-the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal litter decomposer Gymnopus androsaceus and Chalara longipes. We sequenced the genomes of these two fungi, as well as their transcriptomes at different steps of Pinus sylvestris needles decomposition in microcosms. Our results highlighted that if the gene content of the two species could indicate similar potential decomposition abilities, the expression levels of specific gene families belonging to the glycoside hydrolase category reflected contrasting ecological strategies. Actually, C. longipes, the weaker decomposer in this experiment, turned out to have a high content of genes involved in cell wall polysaccharides decomposition but low expression levels, reflecting a versatile ecology compare to the more competitive G. androsaceus with high expression levels of keystone functional genes. Thus, we established that sequential expression of genes coding for different components of the decomposer machinery indicated adaptation to chemical changes in the substrate as decomposition progressed.
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| 3. |
- Bowen, Kathryn J., et al.
(author)
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Implementing the Sustainable Development Goals : towards addressing three key governance challenges-collective action, trade-offs, and accountability
- 2017
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In: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 26-27, s. 90-96
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Research review (peer-reviewed)abstract
- Realising the aspirations of the Sustainable Development Goals (SDGs) to reduce inequality, limit ecological damage, and secure resilient livelihoods is a grand challenge for sustainability science, civil society and government. We identify three key governance challenges that are central for implementing the SDGs: (i) cultivating collective action by creating inclusive decision spaces for stakeholder interaction across multiple sectors and scales; (ii) making difficult trade-offs, focusing on equity, justice and fairness; and (iii) ensuring mechanisms exist to hold societal actors to account regarding decision-making, investment, action, and outcomes. The paper explains each of these three governance challenges, identifying possible avenues for addressing them, and highlights the importance of interlinkages between the three challenges.
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| 4. |
- Gustafsson, Jon-Petter, et al.
(author)
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Where does all the phosphorus go? Mass balance modelling of phosphorus in the Swedish long-term soil fertility experiments
- 2023
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In: Geoderma. - 0016-7061 .- 1872-6259. ; 440
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Journal article (peer-reviewed)abstract
- To gain insights into phosphorus (P) dynamics in soils and the ability to predict soil responses to varying fertilizer inputs, mass balance models prove to be valuable tools. In this study, a new dynamic mass balance model, PBalD8, was used to describe the change in extracted P in the A horizon of soils subjected to diverse fertilizer treatments over a period of 50 to 60 years in five soil fertility experiments. The model employed a Freundlich equation to describe soil-solution partitioning of P and assumed that acid-lactate-extractable P represented a labile pool of P in instant equilibrium with soil solution P. Additionally, oxalate-extractable inorganic P was presumed to comprise the sum of the labile and stable pools of P, with mass flux to and from the latter described by Fick's first law. The model was evaluated using results from extractions and P K-edge XANES spectroscopy. Notably, organic P, as revealed by P K-edge XANES, did not substantially contribute to long-term changes in soil P content and was therefore excluded from consideration. In general, the model offered reasonable fits to the extracted P concentrations. However, for the P-depleted treatments, a prerequisite was that the P removal through harvest was lower compared to measurements. Conversely, in three of the soils, the modelled fertilizer inputs needed to be reduced to 70 % to 85 % of the known additions. These discrepancies may be attributed to the involvement of deeper soil horizons, including deep crop uptake and mixing with lower soil layers, although other factors such as lateral dispersion and inaccuracies in estimating applied fertilizers cannot be discounted. These results underscore the necessity of gaining a more comprehensive understanding of how deeper soil horizons influence P mass balances in agricultural soils. In one of the soils, Fja center dot rdingslo center dot v, P K-edge XANES results demonstrated the formation of calcium phosphate over time in the highest fertilization treatment, consistent with the model. Additionally, in two soils, Kungsa center dot ngen and the P-depleted Vreta Kloster soil, the model predicted a significant contribution from mineral weathering. However, the PBalD8 model also projected higher P leaching rates than those observed, suggesting that the model may not fully capture this P output term.
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| 5. |
- Hasby, Fahri A., et al.
(author)
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Transcriptomic markers of fungal growth, respiration and carbon-use efficiency
- 2021
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In: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 368:15
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Journal article (peer-reviewed)abstract
- Fungal metabolic carbon acquisition and its subsequent partitioning between biomass production and respiration, i.e. the carbon-use efficiency (CUE), are central parameters in biogeochemical modeling. However, current available techniques for estimating these parameters are all associated with practical and theoretical shortcomings, making assessments unreliable. Gene expression analyses hold the prospect of phenotype prediction by indirect means, providing new opportunities to obtain information about metabolic priorities. We cultured four different fungal isolates (Chalara longipes, Laccaria bicolor, Serpula lacrymans and Trichoderma harzianum) in liquid media with contrasting nitrogen availability and measured growth rates and respiration to calculate CUE. By relating gene expression markers to measured carbon fluxes, we identified genes coding for 1,3-beta-glucan synthase and 2-oxoglutarate dehydrogenase as suitable markers for growth and respiration, respectively, capturing both intraspecific variation as well as within-strain variation dependent on growth medium. A transcript index based on these markers correlated significantly with differences in CUE between the fungal isolates. Our study paves the way for the use of these markers to assess differences in growth, respiration and CUE in natural fungal communities, using metatranscriptomic or the RT-qPCR approach.
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