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Sökning: WFRF:(Tunlid Anders)

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1.
  • Rosén, Stefan, et al. (författare)
  • A multispecific saline-soluble lectin from the parasitic fungus Arthrobotrys oligospora. Similarities in the binding specificities compared with a lectin from the mushroom agaricus bisporus.
  • 1996
  • Ingår i: European journal of biochemistry / FEBS. - : Wiley. - 0014-2956 .- 1432-1033. ; 238:3, s. 830-7
  • Tidskriftsartikel (refereegranskat)abstract
    • Several fungi can express high levels of saline-soluble and low-molecular-mass lectins that bind to glycoproteins such as fetuin and different mucins but not bind to any monosaccharides. In this paper, we report the binding specificities of such a lectin (designated AOL) isolated from the nematophagous fungus Arthrobotrys oligospora. The results show that AOL is a multispecific lectin that interacts with the following ligands: (a) Several sulfated glycoconjugates including sulfatide, dextran sulfate, and fucoidan. The specificity of this binding was indicated by experiments showing that none of the tested neutral- and sialic-acid-containing glycolipids, chondroitin sulfates B and C, heparin, and polyvinyl sulfate bound to AOL; (b) Phosphatidic acid and phospatidylglycerol, two out of several tested phospholipids. (c) N-linked and O-linked sugar chains bound to intact fetuin. The involvement of such sugar structures was demonstrated by analyzing the binding of AOL to chemically deglycosylated (trifluoromethanesulfonic acid) fetuin. Treating fetuin with O-glycosidase and N-glycosidase indicated that AOL bound to Gal beta GaLNAc alpha-Ser/Thr and to some N-linked complex sugars, respectively. Further assays demonstrated that AOL could interact with several other glycoproteins containing O-linked and/or N-linked sugar chains. The observations that AOL did not bind to free N-linked sugars isolated from fetuin, or to fetuin treated with trypsin or pronase, or to any of the tested neoglycoproteins and glycolipids with neutral- or sialic acid-containing sugars, indicated that the sugar chains need to be bound to an intact peptide backbone to interact with AOL. We have recently shown that the deduced primary structure of AOL has a high similarity to the sequence of a saline-soluble lectin isolated from the mushroom Agaricus bisporus (ABL) (Rosén, S., Kata, M., Persson, Y., Lipniunas, P. H., Wikström, M., van den Hondel, C. A. M. J. J., van den Brink, J. M., Rask, L., Hedén L.-O. and Tunlid, A., see companion paper). It is well known that ABL binds to Gal beta 3GaLNAc alpha-Ser/Thr, and in this paper we demonstrate that ABL binds to sulfatide, phosphatidic acid, phospatidylglycerol, and possibly also to the same N-linked complex sugars as AOL. The above data indicate that AOL and ABL are members of a novel family of fungal lectins sharing similar primary structure and binding properties.
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2.
  • Valeur, Anders, et al. (författare)
  • Differences in lipid composition between free-living and initially adhered cells of a Gram-negative bacterium
  • 1988
  • Ingår i: Archives of Microbiology. - 0302-8933. ; 149:6, s. 521-526
  • Tidskriftsartikel (refereegranskat)abstract
    • The phospholipid fatty acid composition and poly-β-hydroxybutyrate (PHB) content of initially adhered and free-living cells of a Pseudomonas sp. isolated from the rape plant Brassica napus were examined with gas chromatography (GC). Five different adhesion experiments were made including variations in surface charge (hydrophilic and lipophilic), temperature, media composition and time of adhesion. Lipids and poly-β-hydroxybutyrate (PHB) were extracted with a chloroform-methanol-water mixture, hydrolyzed and esterified with pentafluorobenzyl bromide. Analysis was performed with capillary gas chromatography and flame ionization detection. A pronounced difference in both the ratio saturated/unsaturated fatty acids and in PHB content between free-living and adhered bacteria were found. The free-living bacteria has a significantly smaller ratio of saturated/unsaturated C16 and C18 fatty acids and also a smaller ratio of total C18/total C16 fatty acids. Bacteria adhered to the lipophilic surface had a higher ratio of saturated to unsaturated C16 fatty acids than at the hydrophilic surface. There were no major differences between the treatments regarding the amount of bacteria adhered to the surface or their lipid composition.
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3.
  • Ahrén, Dag, et al. (författare)
  • Comparison of gene expression in trap cells and vegetative hyphae of the nematophagous fungus Monacrosporium haptotylum
  • 2005
  • Ingår i: Microbiology. - : Microbiology Society. - 1465-2080 .- 1350-0872. ; 151:3, s. 789-803
  • Tidskriftsartikel (refereegranskat)abstract
    • Nematode-trapping fungi enter the parasitic stage by developing specific morphological structures called traps. The global patterns of gene expression in traps and mycelium of the fungus Monacrosporium haptotylum were compared. The trap of this fungus is a unicellular spherical structure called the knob, which develops on the apex of a hyphal branch. RNA was isolated from knobs and mycelium and hybridized to a cDNA array containing probes of 2822 EST clones of M. haptotylum. Despite the fact that the knobs and mycelium were grown in the same medium, there were substantial differences in the patterns of genes expressed in the two cell types. In total, 23(.)3% (657 of 2822) of the putative genes were differentially expressed in knobs versus mycelium. Several of these genes displayed sequence similarities to genes known to be involved in regulating morphogenesis and cell polarity in fungi. Among them were several putative homologues for small GTPases, such as rho1, rac1 and ras1, and a rho GDP dissociation inhibitor (rdi1). Several homologues to genes involved in stress response, protein synthesis and protein degradation, transcription, and carbon metabolism were also differentially expressed. In the last category, a glycogen phosphorylase (gph1) gene homologue, one of the most upregulated genes in the knobs as compared to mycelium, was characterized. A number of the genes that were clifferentially expressed in trap cells are also known to be regulated during the development of infection structures in plant-pathogenic fungi. Among them, a gas1 (mas3) gene homologue (designated gks1), which is specifically expressed in appressoria of the rice blast fungus, was characterized.
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4.
  • Ahrén, Dag, et al. (författare)
  • Evolution of parasitism in nematode-trapping fungi
  • 2003
  • Ingår i: Journal of Nematology. - 0022-300X. ; 35:2, s. 194-197
  • Konferensbidrag (refereegranskat)abstract
    • We are studying the evolution of parasitism in a group of soil-living ascomycetes that can grow as saprophytes as well as parasites by forming special morphological structures called traps. Analyses of 18S ribosomal DNA sequences have shown that these fungi form a monophyletic and isolated clade among the ascomycetes. The phylogenetic patterns within this clade are concordant with the morphology of the traps and separate species having adhesive traps (nets, knobs, and branches) from those having constricting rings. This suggests that these nematode-trapping fungi have a common ancestor, and that the ability to capture nematodes has been an important trait for further speciation and diversification within the clade. To obtain information on the genomic basis for this pattern, we recently started a large-scale sequencing project of the nematode-trapping fungus Monacrosporium haptotylum. This will allow the identification of genes uniquely expressed during the development of traps, and elucidate the molecular evolution Of Such genes within the nematode-trapping fungi clade.
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5.
  • Ahrén, Dag, et al. (författare)
  • Low genetic diversity among isolates of the nematode-trapping fungus Duddingtonia flagrans: evidence for recent worldwide dispersion from a single common ancestor
  • 2004
  • Ingår i: Mycological Research. - 0953-7562. ; 108, s. 1205-1214
  • Tidskriftsartikel (refereegranskat)abstract
    • The genetic variation of Duddingtonia flagrans, which has become a promising biocontrol agent of animal parasitic nematodes, was investigated in a worldwide collection of 22 isolates. We analysed the sequence variation in four nuclear genes, tubA (beta-tubulin), CMD1 (calmodulin), EF1alpha (translation elongation factor 1alpha), and PII (extracellular serine protease). 1428 aligned base pairs (bp) were analysed from the four genes, including 709 bp of introns. In addition, the variations in three anonymous genomic regions comprising 1155 bp were examined. Three single nucleotide polymorphisms (SNPs) were detected in the seven loci, none of them in the protein encoding genes. The genetic variation was significantly higher in the nematode-trapping fungus Arthrobotrys oligospora, the closest evolutionary relative to D. flagrans. Analysis of 12 isolates of A. oligospora revealed 30 SNPs in tub A, CMD1, EF1alpha and PII. The genetic variation in the isolates of D. flagrans was further examined using AFLP analysis. Five primer combinations were used to detect 159 bands, of which 94 (59.1%) were polymorphic. A neighbour-joining tree based on the AFLP data showed no clear association between genotype and geographical origin. Furthermore, the AFLP data suggest that D. flagrans is mainly clonal and no recombination could be detected, not even within the same country. The low genetic variation in D. flagrans suggests that this fungus has recently diverged from a single progenitor. Based on estimations of mutation rates, it was calculated that this most recent common ancestor lived about 16000-23000 years ago.
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6.
  • Ahrén, Dag, et al. (författare)
  • PHOREST: a web-based tool for comparative analyses of expressed sequence tag data
  • 2004
  • Ingår i: Molecular Ecology Notes. - : Wiley. - 1471-8278 .- 1471-8286. ; 4:2, s. 311-314
  • Tidskriftsartikel (refereegranskat)abstract
    • Comparative analysis of expressed sequence tags is becoming an important tool in molecular ecology for comparing gene expression in organisms grown in certain environments. Additionally, expressed sequence tag database information can be used for the construction of DNA microarrays and for the detection of single nucleotide polymorphisms. For such applications, we present PHOREST, a web-based tool for managing, analysing and comparing various collections of expressed sequence tags. It is written in PHP (PHP: Hypertext Preprocessor) and runs on UNIX, Microsoft Windows and Macintosh (Mac OS X) platforms.
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7.
  • Ahrén, Dag, et al. (författare)
  • Phylogeny of nematode-trapping fungi based on 18S rDNA sequences
  • 1998
  • Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 158:2, s. 179-184
  • Tidskriftsartikel (refereegranskat)abstract
    • The small subunit (SSU) ribosomal DNA (18S rDNA) from 15 species of nematode-trapping fungi and closely related non-parasitic species were sequenced. Phylogenetic analysis indicated that species within the genera of Arthrobotrys, Dactylaria, Dactylella, Monacrosporium and Duddingtonia formed a monophyletic and isolated clade among an unresolved cluster of apothecial ascomycetes. The phylogenetic patterns within this clade were not concordant with the morphology of the conidia nor the conidiophores, but rather with that of the infection structures. The results from the different methods of tree reconstruction supported three lineages; the species having constricting rings, the non-parasitic species and the species having various adhesive structures (nets, hyphae, knobs and non-constricting rings) to infect nematodes.
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8.
  • Andersson, Erika, et al. (författare)
  • A contrast variation SANS and SAXS study of soil derived dissolved organic matter, and its interactions with hematite nanoparticles
  • 2023
  • Ingår i: JCIS Open. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Soil derived dissolved organic matter (DOM) is an important component of the carbon cycle and influences numerous biogeochemical processes, including the formation of mineral-organic associations. DOM ranges in size from small organic molecules to macromolecules and colloidal aggregates. In this study we have used small angle neutron (SANS) and X-ray (SAXS) scattering to characterize the colloidal DOM fraction from the organic layer of a boreal forest soil, and its interactions with hematite (α-Fe2O3) mineral nanoparticles. Comparison between SAXS and contrast variation SANS patterns revealed that the scattering form factor of the colloidal DOM aggregates was essentially independent of the scattering contrast, implying that the colloidal aggregates have an essentially homogeneous chemical composition, down to the nanometre length scale. Variation of the D2O/H2O ratio of the solvent yielded a SANS intensity minimum at ca. 40 ​vol % D2O, which was consistent with colloids composed of mainly polysaccharides. At pH 5.5 the pure hematite nanoparticles were colloidally stable in water and characterized by a ζ-potential of +25 ​mV and a hydrodynamic radius of ca. 70 ​nm. In the presence of DOM, the hematite nanoparticles lost the colloidal stability and aggregated into larger clusters, displaying a negative ζ-potential of ca. −25 ​mV. The charge reversal suggested that negatively charged polyanions of DOM adsorbed onto the hematite particles, possibly leading to bridging flocculation. Our results suggested that mainly low molecular weight components induced hematite aggregation because no or very limited interactions between DOM colloids and hematite were detected.
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9.
  • Andersson, Erika, et al. (författare)
  • Generation and properties of organic colloids extracted by water from the organic horizon of a boreal forest soil
  • 2023
  • Ingår i: Geoderma. - : Elsevier BV. - 0016-7061. ; 432
  • Tidskriftsartikel (refereegranskat)abstract
    • Organic colloids are an important part of dissolved organic matter (DOM) yet many of their properties remain elusive. The main aims of this study were to assess how the colloidal properties of DOM extracted with water from an organic boreal soil horizon varied with the extraction protocol, and thereby provide insight into the nature of the DOM colloids and develop a mechanistic understanding of how the colloids were generated from the parent soil aggregates. This was accomplished by systematic variations of extraction temperature (4 °C–100 °C), time, mechanical agitation, and pH, together with a combination of chemical analyses, and light and X-ray scattering. Our results agreed with the previous identification of two main colloidal DOM species, one fractal cluster and a second, smaller colloidal DOM species described as chains or coils. Fractal clusters completely dominated the colloidal DOM in extracts from our soil at room temperature and below. Colloidal coils only existed in DOM extracted above room temperature, and their amount increased significantly between 50 °C–100 °C. Moreover, the temperature variation indicated that the fractal clusters partly dissolved into colloidal coils at elevated temperatures. Mechanical agitation at 4 °C significantly increased the amount of DOM extracted, increasing the concentrations of both fractal clusters and low-molecular weight organic compounds. While the clusters were extracted from agitated and non-agitated soil suspensions, the low molecular weight organics were mainly released by agitation. Based on the experimental observations, we propose a conceptual model where parent soil aggregates contain the fractal clusters in mobile and occluded forms, and that the occluded clusters co-exist with occluded low molecular weight organics. These occluded forms may be released by mechanical forces, increasing pH and temperature. At higher temperatures, the soil aggregates and the fractal clusters start to break up, and subsequently individual colloidal coils, presumably carbohydrates, disperse in the water phase. The model explains the origin and properties of the fractal clusters that completely dominate the colloidal DOM extracted from our soil at room temperature and below.
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10.
  • Andersson, Karl-Magnus, et al. (författare)
  • Interspecific and host-related gene expression patterns in nematode-trapping fungi.
  • 2014
  • Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Nematode-trapping fungi are soil-living fungi that capture and kill nematodes using special hyphal structures called traps. They display a large diversity of trapping mechanisms and differ in their host preferences. To provide insights into the genetic basis for this variation, we compared the transcriptome expressed by three species of nematode-trapping fungi (Arthrobotrys oligospora, Monacrosporium cionopagum and Arthrobotrys dactyloides, which use adhesive nets, adhesive branches or constricting rings, respectively, to trap nematodes) during infection of two different plant-pathogenic nematode hosts (the root knot nematode Meloidogyne hapla and the sugar beet cyst nematode Heterodera schachtii).
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11.
  • Andersson, Karl-Magnus, et al. (författare)
  • Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.
  • 2013
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 79:16, s. 4993-5004
  • Tidskriftsartikel (refereegranskat)abstract
    • Many nematophagous fungi use morphological structures called traps to capture nematodes by adhesion or mechanically. To better understand the cellular functions of adhesive traps, the trap cell proteome of the fungus Monacrosporium haptotylum was characterized. The trap of M. haptotylum consists of a unicellular structure called knob that develops at the apex of a hyphae. Proteins extracted from knobs and mycelia were analyzed using SDS-PAGE and LC-MS/MS. The peptide sequences were matched against predicted gene models from the recently sequenced M. haptotylum genome. In total, 336 proteins were identified, with 54 being expressed at significantly higher levels in the knobs than in the mycelia. The upregulated knob proteins included peptidases, small secreted proteins with unknown function and putative cell surface adhesins containing carbohydrate-binding domains including the WSC domain. Phylogenetic analysis showed that all upregulated WSC domain proteins belonged to a large, expanded cluster of paralogs in M. haptotylum. Several peptidases and homologs to experimentally verified proteins in other pathogenic fungi were also upregulated in the knob proteome. Complementary profiling of gene expression at the transcriptome level showed poor correlation between the upregulation of knob proteins and their corresponding transcripts. We propose that the traps of M. haptotylum contain many of the proteins needed in the early stages of infection, and that the trap cells can tightly control the translation and degradation of these proteins to minimize the cost of protein synthesis.
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12.
  • Apoga, D, et al. (författare)
  • Adhesion of conidia and germlings of the plant pathogenic fungus Bipolaris sorokiniana to solid surfaces
  • 2001
  • Ingår i: Mycological Research. - 0953-7562. ; 105:10, s. 1251-1260
  • Tidskriftsartikel (refereegranskat)abstract
    • Soon after coming in contact with its host, the plant pathogenic fungus Bipolaris sorokiniana produces an extracellular material that appears to be important for adhering conidia and germlings to the host surface. To further understand this step of the infection, the adhesion of B. sorokiniana to artificial solid surfaces was examined. On a hydrophobic (polystyrene) surface adhesion occurred in two stages, the first by conidia and the second by germlings. Conidial adhesion occurred shortly (0-1 h) after hydration. The conidia were easily detached by increasing the shear force and including detergents in the washing buffer. As conidia were hydrophobic, these observations indicate that conidial adhesion to polystyrene is due to weak, hydrophobic interaction. The second stage of adhesion was accompanied by conidial germination and occurred 1-2 h after hydration and contact with the surface. Concomitant with the delayed adhesion, the fungus produced an extracellular matrix (ECM). The adhesion of germlings was firm and surface-unspecific since they adhered to both hydrophobic and hydrophilic (glass) surfaces, Except for strong bases, hydrochloric acid and broad-specificity proteases (including Pronase E), none of the hydrolytic enzymes, electrolyte solutions, ionic and hydrophobic detergents and organic solvents removed germlings from the solid surfaces. The adhesion of germlings incubated in the presence of the protein glycosylation inhibitor tunicamycin or the lectins Con A (Concanavalin A) and GNA (from Galanthus nivalis) was significantly reduced, which indicates the involvement of surface glycoproteins in this process. The surface proteins of germlings were labelled with I-125, extracted and analysed by two-dimensional gel electrophoresis. This revealed about 40 surface proteins over a wide pH range (4-10) with molecular masses between 10 and 100 kDa.
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13.
  • Apoga, D, et al. (författare)
  • Analysis of proteins in the extracellular matrix of the plant pathogenic fungus Bipolaris sorokiniana using 2-D gel electrophoresis and MS/MS
  • 2001
  • Ingår i: FEMS Microbiology Letters. - 1574-6968. ; 197:2, s. 145-150
  • Tidskriftsartikel (refereegranskat)abstract
    • A method was developed for isolating and sequencing proteins present in the extracellular matrix (ECM) of germlings and hyphae of filamentous fungi, Surface proteins of the cereal pathogen Bipolaris sorokiniana were labelled with a membrane impermeable biotinylating agent and extracted using a glycine-HCl buffer. Extracted proteins were purified by affinity binding to streptavidin-conjugated magnetic beads or by two-dimensional gel electrophoresis. Four of the biotinylated proteins from the ECM of B. sorokiniana were isolated, in gel digested with trypsin and partly sequenced by tandem mass spectrometry. No significant sequence similarities to proteins in databases were obtained. (C) 2001 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights, reserved.
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14.
  • Balogh, Johanna, et al. (författare)
  • Deletion of a lectin gene does not affect the phenotype of the nematode-trapping fungus Arthrobotrys oligospora
  • 2003
  • Ingår i: Fungal Genetics and Biology. - 1087-1845. ; 39:2, s. 128-135
  • Tidskriftsartikel (refereegranskat)abstract
    • A number of filamentous fungi are known to produce high levels of saline-soluble and low-molecular-mass lectins. The function of these proteins are not clear but it has been proposed that they are involved in storage of nutrients, development, recognition of other organisms, and defense reactions. A gene encoding such a lectin (AOL) was deleted in the nematode-trapping fungus Arthrobotrys oligospora by homologous recombination. The deletion mutants did not express any hemagglutinating activity or protein cross-reacting with AOL antibodies. There were no significant differences between the DeltaAOL and wild-type strains in spore (conidia) germination, saprophytic growth, and pathogenicity. Furthermore, there was no significant difference in the growth and reproduction of collembolan feeding on the various strains of A. oligospora. Thus either the previous proposed functions of AOL are not correct, or the fungus can compensate for the absence of the lectin by expressing other proteins with similar function(s) as AOL. (C) 2003 Published by Elsevier Science (USA).
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15.
  • Bangyeekhun, Eakaphun, 1973- (författare)
  • Parasite on Crayfish : Characterisation of Their Pathogenesis, Host Interactions and Diversity
  • 2002
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The crayfish plague refractory crayfish, Pacifastacus leniusculus, which can harbour the fungal parasite within melanotic sheath, are found to constitutively express the gene encoding for prophenoloxidase (proPO) after mimicking parasite attack. In contrast, the susceptible crayfish, Astacus astacus, responds to the parasite by increased levels of proPO transcript, particularly in the semigranular haemocytes. The upregulation of proPO could confer a temporary resistance towards the fungal infection, suggesting that additional factors are involved in maintaining the balance between host and parasite. The resistant crayfish may have adapted to the parasite by increasing the transcript level of immune genes. The parasite can be considered as a symbiont since it does not harm the host rather than it activates the immune gene and possibly preventing other pathogens to become established.Two serine proteinase genes encoding a subtilisin-like (AaSP1) and a trypsin (AaSP2) enzyme were isolated from the crayfish plague fungus, Aphanomyces astaci. These proteinases are prepropeptides and generate mature proteins of 39 kDa and 29 kDa, respectively. Characterisation of AaSP1 suggests that the enzyme may be involved in intracellular control mechanisms rather than playing a role in pathogenesis. The AaSP2 transcript was not controlled by catabolic repression, but was induced by crayfish plasma, implying a role in pathogenesis toward the crayfish host. Physiology and genetics of five Aphanomyces strains, which were isolated from moribund crayfish, were characterised with regard to their pathogen diversity. These strains are not virulent against crayfish. Some physiological properties of these strains differed from A. astaci, such as growth rate, germination and production of chitinase. Genetic analysis clearly indicated that they are not related to A. astaci and their name are proposed to be Aphanomyces repetans.The crayfish P. leniusculus was found to be susceptible to white spot syndrome virus infection. The virus has a significant effect to the population of crayfish haemocyte. The number and proportion of granular cell from virus-infected crayfish were higher than in controls, indicating granular cells are more resistant to and may interact by some means with the virus.Two morphotypes of the crayfish parasite Psorospermium haeckeli obtained from different crayfish hosts of different geographical origin were analysed for ribosomal ITS DNA in order to compare their genetic diversity. The sequence difference between them was found largely in ITS 1 and ITS 2 regions, which was variable in length and showed 66% and 58% sequence similarity. Thus, different morphotypes of P. haeckeli are genetically diverse.
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16.
  • Bracht Jörgensen, Helene, et al. (författare)
  • Selective foraging of fungi by collembolans in soil
  • 2005
  • Ingår i: Biology letters. - : The Royal Society. - 1744-9561 .- 1744-957X. ; 1:2, s. 243-246
  • Tidskriftsartikel (refereegranskat)abstract
    • Soils contain highly diverse communities of microorganisms and invertebrates. The trophic interactions between these species are largely unknown. Collembolans form an abundant part of the invertebrate community in soils. A prevailing view is that soil collembolans are generalist feeders on fungi, lichens, fragmented litter and bacteria. However, in laboratory food choice experiments, it has been shown that collembolans preferentially select certain taxa of fungi. To examine this apparent contradiction, we developed a molecular technique based on the analysis of 18S ribosomal DNA (rDNA) sequences to explore the diversity of fungi in soils and in the guts of collembolans. We report that the diversity of fungi found in the natural soil was 33 times higher than that in the guts of the collembolan Protaphorura armata. The data support the view that collembolan species can be highly selective when foraging on fungi in soils.
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17.
  • Braesel, Jana, et al. (författare)
  • Three Redundant Synthetases Secure Redox-Active Pigment Production in the Basidiomycete Paxillus involutus.
  • 2015
  • Ingår i: Chemistry and Biology. - : Elsevier BV. - 1879-1301 .- 1074-5521. ; 22:10, s. 1325-1334
  • Tidskriftsartikel (refereegranskat)abstract
    • The symbiotic fungus Paxillus involutus serves a critical role in maintaining forest ecosystems, which are carbon sinks of global importance. P. involutus produces involutin and other 2,5-diarylcyclopentenone pigments that presumably assist in the oxidative degradation of lignocellulose via Fenton chemistry. Their precise biosynthetic pathways, however, remain obscure. Using a combination of biochemical, genetic, and transcriptomic analyses, in addition to stable-isotope labeling with synthetic precursors, we show that atromentin is the key intermediate. Atromentin is made by tridomain synthetases of high similarity: InvA1, InvA2, and InvA5. An inactive atromentin synthetase, InvA3, gained activity after a domain swap that replaced its native thioesterase domain with that of InvA5. The found degree of multiplex biosynthetic capacity is unprecedented with fungi, and highlights the great importance of the metabolite for the producer.
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18.
  • Bååth, Erland, et al. (författare)
  • Microbial community-based measurements to estimate heavy metal effects in soil : The use of phospholipid fatty acid patterns and bacterial community tolerance
  • 1998
  • Ingår i: Ambio: a Journal of Human Environment. - 0044-7447. ; 27:1, s. 58-61
  • Tidskriftsartikel (refereegranskat)abstract
    • Microbial community-based measurements to detect effects of heavy metals in soils rely on the premise that metal toxicity exerts a selection pressure, which induces a change in the composition of the community. The phospholipid fatty acid (PLFA) composition gives an integrated picture of all living organisms in the soil, and changes in the PLFA pattern of the soil indicate an altered species composition due to, e.g. metal toxicity. An increased bacterial community tolerance to metals also indicates an altered community composition, with tolerant organisms becoming more abundant relative to sensitive organisms. The use of these two techniques is described, and their advantages and disadvantages as monitoring tools are discussed and exemplified by field data and laboratory experiments from different soils.
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19.
  • Börjesson, Gunnar, et al. (författare)
  • Methane oxidation in landfill cover soils, as revealed by potential oxidation measurements and phospholipid fatty acid analyses
  • 1998
  • Ingår i: Soil Biology and Biochemistry. - 0038-0717. ; 30:10-11, s. 1423-1433
  • Tidskriftsartikel (refereegranskat)abstract
    • Landfills account for ca. 10% of the annual global burden of atmospheric methane. Part of the efflux is mitigated by means of biological methane oxidation in the landfill covers. In this study, two types of landfill cover soils (mineral soil and sewage sludge) were compared with respect to methane emissions as well as potential methane oxidation capacity and the PLFA (phospholipid fatty acid) content of soil samples. Methane fluxes were lowest at a landfill site where wastes were covered with old sewage sludge. This site consumed atmospheric methane on most occasions. In incubated soil samples from the landfill cover composed of mineral soil, potential methane oxidation was most strongly correlated with the concentration of PLFA 18:1ω8, which is typical for type-II methanotrophic bacteria. In contrast, in samples from a landfill cover composed of fresh sewage sludge, methane oxidation was most strongly correlated with 16:1-PLFAs, indicating that type-I methanotrophs predominated, probably owing to nutritional conditions being more favourable in the sludge. The results also indicate that it takes a long time, i.e. several years, for methanotrophs to get well established in landfill cover soils.
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20.
  • Börjesson, Gunnar, et al. (författare)
  • Microbial oxidation of CH4 at high partial pressures in an organic landfill cover soil under different moisture regimes
  • 1998
  • Ingår i: FEMS Microbiology Ecology. - 0168-6496. ; 26:3, s. 207-217
  • Tidskriftsartikel (refereegranskat)abstract
    • The uptake and utilization of CH4 at high concentrations (5-18% vol.) and different soil moistures were followed for samples from a landfill cover soil with a high organic matter content. Measurements of the utilization of CH4 and O2, and production of CO2 indicated that the activity of methanotrophic organisms accounted for most of the O2 respiration. At water saturation, CH4 oxidation rates decreased with time, probably because NH4/+ accumulated. Denitrification rates, estimated based on both N2 and N2O production, were positively related to soil moisture and only slightly influenced by the extent of CH4 oxidation. Total phospholipid fatty acid concentrations increased, and concentrations of phospholipid fatty acids, typical for obligate methanotrophic bacteria (e.g. 16:1ω8 and 18:1ω8), increased in the CH4-amended samples, indicating growth of both type I and type II methanotrophs.
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21.
  • Canbäck, Björn, et al. (författare)
  • The Littorina sequence database (LSD) - an online resource for genomic data.
  • 2012
  • Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 12, s. 142-148
  • Tidskriftsartikel (refereegranskat)abstract
    • We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147 491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26 537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/.
  •  
22.
  • De Beeck, Michiel Op, et al. (författare)
  • Elucidating fungal decomposition of organic matter at sub-micrometer spatial scales using optical photothermal infrared (O-PTIR) microspectroscopy
  • 2024
  • Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 90:2
  • Tidskriftsartikel (refereegranskat)abstract
    • In microbiological studies, a common goal is to link environmental factors to microbial activities. Both environmental factors and microbial activities are typically derived from bulk samples. It is becoming increasingly clear that such bulk environmental parameters poorly represent the microscale environments microorganisms experience. Using infrared (IR) microspectroscopy, the spatial distribution of chemical compound classes can be visualized, making it a useful tool for studying the interactions between microbial cells and their microenvironments. The spatial resolution of conventional IR microspectroscopy has been limited by the diffractionlimit of IR light. The recent development of optical photothermal infrared (O-PTIR) microspectroscopy has pushed the spatial resolution of IR microspectroscopy beyond this diffractionlimit, allowing the distribution of chemical compound classes to be visualized at sub-micrometer spatial scales. To examine the potential and limitations of O-PTIR microspectroscopy to probe the interactions between fungal cells and their immediate environments, we imaged the decomposition of cellulose filmsby cells of the ectomycorrhizal fungus Paxillus involutus and compared O-PTIR results using conventional IR microspectroscopy. Whereas the data collected with conventional IR microspectroscopy indicated that P. involutus has only a very limited ability to decompose cellulose films,O-PTIR data suggested that the ability of P. involutus to decompose cellulose was substantial. Moreover, the O-PTIR method enabled the identificationof a zone located outside the fungal hyphae where the cellulose was decomposed by oxidation. We conclude that O-PTIR can provide valuable new insights into the abilities and mechanisms by which microorganisms interact with their surrounding environments.
  •  
23.
  • de Fine Licht, Henrik Hjarvard, et al. (författare)
  • Symbiotic adaptations in the fungal cultivar of leaf-cutting ants.
  • 2014
  • Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • Centuries of artificial selection have dramatically improved the yield of human agriculture; however, strong directional selection also occurs in natural symbiotic interactions. Fungus-growing attine ants cultivate basidiomycete fungi for food. One cultivar lineage has evolved inflated hyphal tips (gongylidia) that grow in bundles called staphylae, to specifically feed the ants. Here we show extensive regulation and molecular signals of adaptive evolution in gene trancripts associated with gongylidia biosynthesis, morphogenesis and enzymatic plant cell wall degradation in the leaf-cutting ant cultivar Leucoagaricus gongylophorus. Comparative analysis of staphylae growth morphology and transcriptome-wide expressional and nucleotide divergence indicate that gongylidia provide leaf-cutting ants with essential amino acids and plant-degrading enzymes, and that they may have done so for 20-25 million years without much evolutionary change. These molecular traits and signatures of selection imply that staphylae are highly advanced coevolutionary organs that play pivotal roles in the mutualism between leaf-cutting ants and their fungal cultivars.
  •  
24.
  • Diez, A A, et al. (författare)
  • The Escherichia coli ftsK1 mutation attenuates the induction of sigma(s)-dependent genes upon transition to stationary phase
  • 2002
  • Ingår i: FEMS Microbiology Letters. - 1574-6968. ; 206:1, s. 19-23
  • Tidskriftsartikel (refereegranskat)abstract
    • A mutation in the cell division gene ftsK causes super-induction of sigma(70)-dependent stress defense genes, such as uspA, during entry of cells into stationary phase. In contrast, we report here that stationary phase induction of sigma(S)-dependent genes, uspB and cfa, is attenuated and that sigma(S) accumulates at a lower rate in ftsK1 cells. Ectopic overexpression of rpoS restored induction of the rpoS regulon in the ftsK mutant, as did a deletion in the recA gene. Thus, a mutation in the cell division gene,ftsY, uncouples the otherwise coordinated induction of sigma(S)-dependent genes and the universal stress response gene, uspA, during entry into stationary phase. (C) 2002 Federation of European Microbiological Societies, Published by Elsevier Science B.V. All rights reserved.
  •  
25.
  • Ellström, Magnus, et al. (författare)
  • The carbon starvation response of the ectomycorrhizal fungus Paxillus involutus.
  • 2015
  • Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941. ; 91:4
  • Tidskriftsartikel (refereegranskat)abstract
    • The amounts of carbon allocated to the fungal partner in ectomycorrhizal associations can vary substantially depending on the plant growth and the soil nutrient conditions, and the fungus may frequently be confronted with limitations in carbon. We used chemical analysis and transcriptome profiling to examine the physiological response of the ectomycorrhizal fungus Paxillus involutus to carbon starvation during axenic cultivation. Carbon starvation induced a decrease in the biomass. Concomitantly, ammonium, cell-wall material (chitin) and proteolytic enzymes were released into the medium, which suggest autolysis. Compared with the transcriptome of actively growing hyphae, about 45% of the transcripts analyzed were differentially regulated during C-starvation. Induced during starvation were transcripts encoding extracellular enzymes such as peptidases, chitinases, and laccases. In parallel, transcripts of N-transporters were upregulated, which suggest that some of the released nitrogen compounds were re-assimilated by the mycelium. The observed changes suggest that the carbon-starvation response in P. involutus is associated with complex cellular changes that involves autolysis, recycling of intracellular compounds by autophagy and reabsorption of the extracellular released material. The study provides molecular markers that can be used to examine the role of autolysis for the turnover and survival of the ectomycorrhizal mycelium in soils.
  •  
26.
  • Fekete, Csaba, et al. (författare)
  • Paralysis of nematodes: shifts in the transcriptome of the nematode-trapping fungus Monacrosporium haptotylum during infection of Caenorhabditis elegans
  • 2008
  • Ingår i: Environmental Microbiology. - : Wiley. - 1462-2920 .- 1462-2912. ; 10:2, s. 364-375
  • Tidskriftsartikel (refereegranskat)abstract
    • The transcriptional response in the parasitic fungus Monacrosporium haptotylum and its nematode host Caenorhabditis elegans were analyzed during infection using cDNA microarrays. The array contained 2,684 fungal and 372 worm gene reporters. Dramatic shifts occurred in the transcriptome of M. haptotylum during the different stages of the infection. An initial transcriptional response was recorded after 1h of infection when the traps adhered to the cuticle, but before immobilization of the captured nematodes. Among the differentially expressed genes were two serine proteases (spr1 and spr2), and several homologues to genes known to be regulated in other pathogenic fungi. After 4 hours, when approximately 40 % of the nematodes were paralyzed, we identified an up-regulated cluster of 372 fungal genes which were not regulated during the other phases of the infection. This cohort contained a large proportion (79%) of genes that appear to be specific for M. haptotylum and closely related species. These genes were of two different classes; those translating into presumably functional peptides and those with no apparent protein coding potential (noncoding RNAs). Among the infection-induced C. elegans genes were those encoding antimicrobial peptides, protease inhibitors and lectins.
  •  
27.
  • Floudas, Dimitrios, et al. (författare)
  • Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi
  • 2020
  • Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 14:8, s. 2046-2059
  • 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.
  •  
28.
  • Floudas, Dimitrios, et al. (författare)
  • X-ray scattering reveals two mechanisms of cellulose microfibril degradation by filamentous fungi
  • 2022
  • Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 88:17
  • 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.
  •  
29.
  • Frostegard, Asa, et al. (författare)
  • Use and misuse of PLFA measurements in soils
  • 2011
  • Ingår i: Soil Biology & Biochemistry. - : Elsevier BV. - 0038-0717. ; 43:8, s. 1621-1625
  • Tidskriftsartikel (refereegranskat)abstract
    • The determination of the phospholipid fatty acid (PLFA) pattern of soil organisms has become one of the most commonly used methods to study microbial community structure. Here we recapitulate the background of our work applying the PLFA method to soil in the early 1990s. We also stress that although the PLFA method was, and still is, a rapid and sensitive method to detect changes in the microbial community in soil, as with all popular methods it can be misused. We discuss problems in PLFA interpretation, the extent of turn-over of PLFAs in soil, and the flawed use of diversity indices to evaluate PLFA patterns. (C) 2010 Elsevier Ltd. All rights reserved.
  •  
30.
  • Gentile, Luigi, et al. (författare)
  • Ferrihydrite Nanoparticle Aggregation Induced by Dissolved Organic Matter
  • 2018
  • Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 122:38, s. 7730-7738
  • Tidskriftsartikel (refereegranskat)abstract
    • Ferrihydrite (Fh) nanoparticles are omnipresent in nature and often highly mobile because of their colloidal stability. Thus, Fh serves as a vector for iron as well as associated nutrients and contaminants. Here, we demonstrate, using small-angle X-ray scattering combined with cryo-transmission electron microscopy (cryo-TEM), that dissolved organic matter (DOM), extracted from a boreal forest soil, induce aggregation of Fh nanoparticles, of radius 3 nm, into fractal aggregates, having a fractal dimension D = 1.7. The DOM consists of both fractal-like colloids (>100 nm) and small molecular DOM, but the attractive Fh interparticle interaction was mediated by molecular DOM alone as shown by cryo-TEM. This highlights the importance of using soil extracts, including all size fractions, in studies of the colloidal behavior of DOM-mineral aggregates. The Fh nanoparticles also self-assemble during synthesis into aggregates with the same fractal dimension as the DOM-Fh aggregates. We propose that, in both the absence and presence of DOM, the aggregation is controlled by the Fh particle charge, and the process can be viewed as a linear polymerization into a self-avoiding random walk structure. The theoretical D value for this is 5/3, which is in close agreement with our Fh and DOM-Fh results.
  •  
31.
  • Gentile, Luigi, et al. (författare)
  • Fungal decomposition and transformation of molecular and colloidal fractions of dissolved organic matter extracted from boreal forest soil
  • 2024
  • Ingår i: Soil Biology and Biochemistry. - 0038-0717. ; 195
  • 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.
  •  
32.
  • Gunnarsson, Torsten, et al. (författare)
  • Recycling of fecal pellets in isopods : Microorganisms and nitrogen compounds as potential food for Oniscus asellus L
  • 1986
  • Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717. ; 18:6, s. 595-600
  • Tidskriftsartikel (refereegranskat)abstract
    • The isopod Oniscus asellus was fed wood pieces. The fecal pellets produced during 6 days were reingested twice. Both fresh and ageing pellets were examined for microorganisms and nitrogen compounds including proteins and bacterial cell wall compounds, d-alanine and diaminopimelic acid. In old pellets, the plate counts of fungi decreased but that of bacteria as well as the concentrations of proteins and bacterial cell wall compounds increased from the first to the third gut passage. Immediately after a gut passage, the counts of microorganisms were lower than before the passage whereas the concentrations of bacterial cell wall compounds and proteins were higher. This indicates that both growth and lysis of bacteria occurred in the guts but that a considerable part of the bacterial cells were not digested and assimilated by the isopods. Comparison of the bacterial cell wall compounds also indicated shifts in the ratio of Gram-positive and Gram-negative bacteria during gut passages and during ageing of the fecal pellets. The concentration of total N did not markedly change after the second and third gut passages, indicating that the availability of N decreased due to accumulation of N into relatively recalcitrant proteins and bacterial cell walls.
  •  
33.
  • Harish, Ajith, et al. (författare)
  • Rooted phylogeny of the three superkingdoms.
  • 2013
  • Ingår i: Biochimie. - : Elsevier BV. - 1638-6183 .- 0300-9084. ; 95:8, s. 1593-1604
  • Tidskriftsartikel (refereegranskat)abstract
    • The traditional bacterial rooting of the three superkingdoms in sequence-based gene trees is inconsistent with new phylogenetic reconstructions based on genome content of compact protein domains. We find that protein domains at the level of the SCOP superfamily (SF) from sequenced genomes implement with maximum parsimony fully resolved rooted trees. Such genome content trees identify archaea and bacteria (akaryotes) as sister clades that diverge from an akaryote common ancestor, LACA. Several eukaryote sister clades diverge from a eukaryote common ancestor, LECA. LACA and LECA descend in parallel from the most recent universal common ancestor (MRUCA), which is not a bacterium. Rather, MRUCA presents 75% of the unique SFs encoded by extant genomes of the three superkingdoms, each encoding a proteome that partially overlaps all others. This alone implies that the common ancestor to the superkingdoms was very complex. Such ancestral complexity is confirmed by phylogenetic reconstructions. In addition, the divergence of proteomes from the complex ancestor in each superkingdom is both reductive in numbers of unique SFs as well as cumulative in the abundance of surviving SFs. These data suggest that the common ancestor was not the first cell lineage and that modern global phylogeny is the crown of a "recently" re-rooted tree. We suggest that a bottlenecked survivor of an environmental collapse, which preceded the flourishing of the modern crown, seeded the current phylogenetic tree.
  •  
34.
  • Hedh, Jenny, et al. (författare)
  • Multiple gene genealogies and species recognition in the ectomycorrhizal fungus Paxillus involutus.
  • 2008
  • Ingår i: Mycological Research. - : Elsevier BV. - 0953-7562. ; 112:8, s. 965-975
  • Tidskriftsartikel (refereegranskat)abstract
    • Paxillus involutus (basidiomycetes, Boletales) is a common ectomycorrhizal fungus in the Northern Hemisphere. The fungus displays significant variation in phenotypic characters related to morphology, physiology, and ecology. Previous studies have shown that P. involutus contains several intersterility groups and morphological species. In this study, we have used concordance of multiple gene genealogies to identify genetically isolated species of P. involutus. Fragments from five protein coding genes in 50 isolates of P. involutus collected from different hosts and environments in Europe and one location in Canada were analysed using phylogenetic methods. Concordance of the five gene genealogies showed that P. involutus comprises at least four distinct phylogenetic lineages: phylogenetic species I (with nine isolates), II (33 isolates), III (three isolates), and IV (five isolates). The branches separating the four species were long and well supported compared with the species internodes. A low level of shared polymorphisms was observed among the four lineages indicating a long time since the genetic isolation began. Three of the phylospecies corresponded to earlier identified morphological species: I to P. obscurosporus, II to P. involutus s. str., and III to P. validus. The phylogenetic species had an overlapping geographical distribution. Species I and II differed partly in habitat and host preferences.
  •  
35.
  • Hedh, Jenny, et al. (författare)
  • Variation in host specificity and gene content in strains from genetically isolated lineages of the ectomycorrhizal fungus Paxillus involutus s. lat.
  • 2009
  • Ingår i: Mycorrhiza. - : Springer Science and Business Media LLC. - 1432-1890 .- 0940-6360. ; 19, s. 549-558
  • Tidskriftsartikel (refereegranskat)abstract
    • Ectomycorrhizal fungi are known to vary in host range. Some fungi can enter into symbiosis with multiple plant species, while others have restricted host ranges. The aim of this study was to examine variation in host specificity among strains from the basidiomycete Paxillus involutus s. lat. Recent studies have shown that this fungus consists of at least four genetically isolated lineages, phylogenetic species (PS) I (which corresponds to the morphological species Paxillus obscurosporus), PS II (P. involutus s. str.), PS III (Paxillus validus), and PS IV (not yet supported by any reference material). Thirty-five Paxillus strains of PS I to IV were examined in microcosms for their capacity to infect birch (Betula pendula) and spruce (Picea abies). Seventeen strains were compatible and formed mycorrhizae with both tree species. Seven strains were incompatible with both birch and spruce. The gene content in three pairs of incompatible and compatible strains PS I, II, and III were compared using microarray-based comparative genomic hybridizations. Of 4,113 P. involutus gene representatives analyzed, 390 varied in copy numbers in at least one of the three pairwise comparisons. Only three reporters showed significant changes in all three pairwise comparisons, and none of these were changed in a similar way in three comparisons. Our data indicate that changes in host range have occurred frequently and independently among strains in P. obscurosporus, P. involutus s. str., and P. validus. No evidence was obtained demonstrating that these changes have been associated with the gain or loss of similar genes in these three species.
  •  
36.
  • Hertz, Birgit, et al. (författare)
  • Nematophagous Fungi
  • 2000
  • Ingår i: Encyclopedia of Life Science (ELS). - 047001590X
  • Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
    • Abstract is not available
  •  
37.
  • Johansson, Tomas, et al. (författare)
  • Transcriptional responses of Paxillus involutus and Betula pendula during formation of ectomycorrhizal root tissue
  • 2004
  • Ingår i: Molecular Plant-Microbe Interactions. - 0894-0282 .- 1943-7706. ; 17:2, s. 202-215
  • Tidskriftsartikel (refereegranskat)abstract
    • In order to obtain information on genes specifically expressed in the ectomycorrhizal symbiosis, 3,555 expressed sequence tags (ESTs) were analyzed from a cDNA library constructed from ectomycorrhiza formed between the basidiomycete Paxillus involutus and birch (Betula pendula). cDNA libraries from saprophytically growing fungus (3,964 ESTs) and from axenic plants (2,532 ESTs) were analyzed in parallel. By clustering all the EST obtained, a nonredundant set of 2,284 unique transcripts of either fungal or plant origin were identified. The expression pattern of these genes was analyzed using cDNA microarrays. The analyses showed that the plant and fungus responded to the symbiosis by altering the expression levels of a number of enzymes involved in carbon metabolism. Several plant transcripts with sequence similarities to genes encoding enzymes in the tricarboxylic cycle and electron transport chain were down regulated as compared with the levels in free-living roots. In the fungal partner, a number of genes encoding enzymes in the lipid and secondary metabolism were down regulated in mycorrhiza as compared with the saprophytically growing mycelium. A substantial number of the ESTs analyzed displayed significant sequence similarities to proteins involved in biotic stress responses, but only a few of them showed differential expression in the mycorrhizal tissue, including plant and fungal metallothioneins and a plant defensin homologue. Several of the genes that were differentially expressed in the mycorrhizal root tissue displayed sequence similarity to genes that are known to regulate growth and development of plant roots and fungal hyphae, including transcription factors and Rho-like GTPases.
  •  
38.
  • Kohler, Annegret, et al. (författare)
  • Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
  • 2015
  • Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 176-410
  • 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.
  •  
39.
  • Krumina, Lelde, et al. (författare)
  • Ectomycorrhizal Fungal Transformation of Dissolved Organic Matter : Consequences for Reductive Iron Oxide Dissolution and Fenton-Based Oxidation of Mineral-Associated Organic Matter
  • 2022
  • Ingår i: Frontiers in Earth Science. - : Frontiers Media SA. - 2296-6463. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • Recent studies have shown that dissolved organic matter (DOM) decomposed by ectomycorrhizal (ECM) fungi increases adsorptive properties of organic matter towards soil mineral surfaces. Concomitantly, ECM fungi secrete secondary metabolites with iron reducing capacity that are thought to participate in non-enzymatic Fenton-based decomposition of DOM. The aim of this study was to investigate if the iron reduction induced by the ECM fungus Paxillus involutus during organic matter decomposition was conserved in the decomposed DOM. We explored how the modified DOM reductively dissolved ferrihydrite and goethite nanoparticles and how these processes affected the reactions with H2O2 and the Fenton-based oxidation of mineral-associated organic matter. Culture filtrates were obtained from incubation of the ECM fungus on DOM from forest litter of a spruce forest. This modified DOM was separated by extraction into an ethyl acetate and a water fraction. These fractions were reacted with ferrihydrite and goethite in absence and presence of H2O2. Dissolved Fe2+ and HO• were measured and the reactions at the iron oxide-water interfaces were monitored in real-time with in-situ IR spectroscopy. Experiments showed that decomposition of DOM by P. involutus generated a modified DOM that displayed an increased and persistent reductive capacity. Most of the reductants were isolated in the aromatic- and carboxyl-dominated ethyl acetate fraction but some reduction capacity was also captured in the water fraction mainly containing carbohydrates. Reductive dissolution was more extensive for ferrihydrite than goethite, and this process generated significant oxidation of the DOM-ferrihydrite associations. Oxidation of adsorbed DOM was triggered by H2O2 via heterogenous and homogeneous Fenton reactions. These oxidation processes were favored by ferrihydrite because of a high reduction potential and a high efficiency of heterogeneous Fenton as compared to goethite. An optimal timing between the heterogeneous and homogeneous Fenton processes triggered extensive radical oxidation of the DOM-ferrihydrite associations generating a high concentration of surface-associated oxalate. Overall, the results show that organic matter associated with ferrihydrite may be more susceptible to radical oxidation than on goethite, and that fungal decomposition of DOM in general may have consequences for other important soil processes such as mineral dissolution, adsorption and initiation of radical reactions.
  •  
40.
  • Krumina, Lelde, et al. (författare)
  • Oxidation of a Dimethoxyhydroquinone by Ferrihydrite and Goethite Nanoparticles : Iron Reduction versus Surface Catalysis
  • 2017
  • Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 51:16, s. 9053-9061
  • Tidskriftsartikel (refereegranskat)abstract
    • Hydroquinones are important mediators of electron transfer reactions in soils with a capability to reduce Fe(III) minerals and molecular oxygen, and thereby generating Fenton chemistry reagents. This study focused on 2,6-dimethoxy hydroquinone (2,6-DMHQ), an analogue to a common fungal metabolite, and its reaction with ferrihydrite and goethite under variable pH and oxygen concentrations. Combined wet-chemical and spectroscopic analyses showed that both minerals effectively oxidized 2,6-DMHQ in the presence of oxygen. Under anaerobic conditions the first-order oxidation rate constants decreased by one to several orders of magnitude depending on pH and mineral. Comparison between aerobic and anaerobic results showed that ferrihydrite promoted 2,6-DMHQ oxidation both via reductive dissolution and heterogeneous catalysis while goethite mainly caused catalytic oxidation. These results were in agreement with changes in the reduction potential (EH) of the Fe(III) oxide/Fe(II)aq redox couple as a function of dissolved Fe(II) where EH of goethite was lower than ferrihydrite at any given Fe(II) concentration, which makes ferrihydrite more prone to reductive dissolution by the 2,6-DMBQ/2,6-DMHQ redox couple. This study showed that reactions between hydroquinones and iron oxides could produce favorable conditions for formation of reactive oxygen species, which are required for nonenzymatic Fenton-based decomposition of soil organic matter.
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41.
  • Ladygina, Natalia, et al. (författare)
  • Diversity of bacteria associated with grassland soil nematodes of different feeding groups.
  • 2009
  • Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 69:1, s. 53-61
  • Tidskriftsartikel (refereegranskat)abstract
    • Abstract The bacterial diversity associated with soil nematodes and its relationship with their feeding habits are as yet poorly understood. In the present study the diversity and abundance of bacteria from nematodes and their surrounding soil were analysed and compared. The nematodes were collected from a grassland soil and sorted into bacterial, fungal, plant, predatory and omnivore feeding groups and assigned to taxonomic groups. Total DNA was extracted from the nematodes and partial bacterial 16S rRNA genes were PCR amplified, cloned and sequenced. The abundance and composition of bacterial taxa differed between and within feeding groups. The lowest bacterial diversity was found in the predatory nematodes Prionchulus sp., whereas the highest bacterial diversity was associated with the bacterial-feeding nematode Acrobeles sp. The soil had a more diverse bacterial community than the communities found in the nematode groups. The 16S rRNA gene sequences of bacteria associated with nematodes did not overlap with those detected in soil as determined using the cloning screening approach. However, bacterial sequences identified from nematodes could be detected in the soil with targeted PCR. Our data suggest that the nematodes do not feed on the most abundant bacteria present in soil. Furthermore, several nematodes contained suspected bacterial symbionts and parasites.
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42.
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43.
  • Le Quéré, Antoine, et al. (författare)
  • Divergence in gene expression related to variation in host specificity of an ectomycorrhizal fungus
  • 2004
  • Ingår i: Molecular Ecology. - 0962-1083. ; 13:12, s. 3809-3819
  • Tidskriftsartikel (refereegranskat)abstract
    • Ectomycorrhizae are formed by mutualistic interactions between fungi and the roots of woody plants. During symbiosis the two organisms exchange carbon and nutrients in a specific tissue that is formed at the contact between a compatible fungus and plant. There is considerable variation in the degree of host specificity among species and strains of ectomycorrhizal fungi. In this study, we have for the first time shown that this variation is associated with quantitative differences in gene expression, and with divergence in nucleotide sequences of symbiosis-regulated genes. Gene expression and sequence evolution were compared in different strains of the ectomycorrhizal fungus Paxillus involutus; the strains included Nau, which is not compatible with birch and poplar, and the two compatible strains Maj and ATCC200175. On a genomic level, Nau and Maj were very similar. The sequence identity was 98.9% in the 16 loci analysed, and only three out of 1075 genes analysed by microarray-based hybridizations had signals indicating differences in gene copy numbers. In contrast, 66 out of the 1075 genes were differentially expressed in Maj compared to Nau after contact with birch roots. Thirty-seven of these symbiosis-regulated genes were also differentially expressed in the ATCC strain. Comparative analysis of DNA sequences of the symbiosis-regulated genes in different strains showed that two of them have evolved at an enhanced rate in Nau. The sequence divergence can be explained by a decreased selection pressure, which in turn is determined by lower functional constraints on these proteins in Nau as compared to the compatible strains.
  •  
44.
  • Le Quéré, Antoine, et al. (författare)
  • Global patterns of gene regulation associated with the development of ectomycorrhiza between birch (Betula pendula Roth.) and Paxillus involutus (Batsch) fr.
  • 2005
  • Ingår i: Molecular Plant-Microbe Interactions. - 0894-0282. ; 18:7, s. 659-673
  • Tidskriftsartikel (refereegranskat)abstract
    • The formation of ectomycorrhizal (ECM) root tissue is characterized by distinct morphological and developmental stages, such as preinfection and adhesion, mantle, and Hartig net formation. The global pattern of gene expression during these stages in the birch (Betula pendula)-Paxillus involutus ECM association was analyzed using cDNA microarrays. In comparison with nonsymbiotic conditions, 251 fungal (from a total of 1,075) and 138 plant (1,074 in total) genes were found to be differentially regulated during the ECM development. For instance, during mantle and Hartig net development, there were several plant genes upregulated that are normally involved in defense responses during pathogenic fungal challenges. These responses were, at later stages of ECM development, found to be repressed. Other birch genes that showed differential regulation involved several homologs that usually are implicated in water permeability (aquaporins) and water stress tolerance (dehydrins). Among fungal genes differentially upregulated during stages of mantle and Hartig net formation were homologs putatively involved in mitochondrial respiration. In fully developed ECM tissue, there was an upregulation of fungal genes related to protein synthesis and the cytoskeleton assembly machinery. This study highlights complex molecular interactions between two symbionts during the development of an ECM association.
  •  
45.
  • Le Quéré, Antoine, et al. (författare)
  • Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays
  • 2006
  • Ingår i: Molecular Ecology. - 0962-1083. ; 15:2, s. 535-550
  • Tidskriftsartikel (refereegranskat)abstract
    • We have examined the variations in gene content and sequence divergence that could be associated with symbiotic adaptations in the ectomycorrhizal fungus Paxillus involutus and the closely related species Paxillus filamentosus. Strains with various abilities to form mycorrhizae were analysed by comparative genomic hybridizations using a cDNA microarray containing 1076 putative unique genes of P. involutus. To screen for genes diverging at an enhanced and presumably non-neutral rate, we implemented a simple rate test using information from both the variations in hybridizations signal and data on sequence divergence of the arrayed genes relative to the genome of Coprinus cinereus. C. cinereus is a free-living saprophyte and is the closest evolutionary relative to P. involutus that has been fully sequenced. Approximately 17% of the genes investigated were detected as rapidly diverging within Paxillus. Furthermore, 6% of the genes varied in copy numbers between the analysed strains. Genome rearrangements associated with this variation including duplications and deletions may also play a role in adaptive evolution. The cohort of divergent and duplicated genes showed an over-representation of either orphans, genes whose products are located at membranes, or genes encoding for components of stress/defence reactions. Some of the identified genomic changes may be associated with the variation in host specificity of ectomycorrhizal fungi. The proposed procedure could be generally applicable to screen for rapidly evolving genes in closely related strains or species where at least one has been sequenced or characterized by expressed sequence tag analysis.
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46.
  • Le Quéré, Antoine, et al. (författare)
  • Size and complexity of the nuclear genome of the ectomycorrhizal fungus Paxillus involutus.
  • 2002
  • Ingår i: Fungal Genetics and Biology. - 1087-1845. ; 36:3, s. 234-241
  • Tidskriftsartikel (refereegranskat)abstract
    • The basidiomycete Paxillus involutus is forming ectomycorrhizal symbiosis with a broad range of forest trees. Reassociation kinetics on P. involutus nuclear DNA indicated a haploid genome size of 23Mb including 11% of repetitive DNA. A similar genome size (20Mb) was estimated by genomic reconstruction analysis using three single copy genes. To assess the gene density in the P. involutus genome, a cosmid containing a 33-kb fragment of genomic DNA was sequenced and used to identify putative open reading frames (ORFs). Twelve potential ORFs were predicted, eight displayed significant sequence similarities to known proteins found in other organisms and notably, several homologues to the Podospora anserina vegetative incompatibility protein (HetE1) were found. By extrapolation, we estimate the total number of genes in the P. involutus haploid genome to approximately 7700.
  •  
47.
  • Li, Yuan, et al. (författare)
  • Evidence for Positive Selection within the PgiC1 Locus in the Grass Festuca ovina.
  • 2015
  • Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
  • Tidskriftsartikel (refereegranskat)abstract
    • The dimeric metabolic enzyme phosphoglucose isomerase (PGI, EC 5.3.1.9) plays an essential role in energy production. In the grass Festuca ovina, field surveys of enzyme variation suggest that genetic variation at cytosolic PGI (PGIC) may be adaptively important. In the present study, we investigated the molecular basis of the potential adaptive significance of PGIC in F. ovina by analyzing cDNA sequence variation within the PgiC1 gene. Two, complementary, types of selection test both identified PGIC1 codon (amino acid) sites 200 and 173 as candidate targets of positive selection. Both candidate sites involve charge-changing amino acid polymorphisms. On the homology-modeled F. ovina PGIC1 3-D protein structure, the two candidate sites are located on the edge of either the inter-monomer boundary or the inter-domain cleft; examination of the homology-modeled PGIC1 structure suggests that the amino acid changes at the two candidate sites are likely to influence the inter-monomer interaction or the domain-domain packing. Biochemical studies in humans have shown that mutations at several amino acid sites that are located close to the candidate sites in F. ovina, at the inter-monomer boundary or the inter-domain cleft, can significantly change the stability and/or kinetic properties of the PGI enzyme. Molecular evolutionary studies in a wide range of other organisms suggest that PGI amino acid sites with similar locations to those of the candidate sites in F. ovina may be the targets of positive/balancing selection. Candidate sites 200 and 173 are the only sites that appear to discriminate between the two most common PGIC enzyme electromorphs in F. ovina: earlier studies suggest that these electromorphs are implicated in local adaptation to different grassland microhabitats. Our results suggest that PGIC1 sites 200 and 173 are under positive selection in F. ovina.
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48.
  • Lindahl, Björn, et al. (författare)
  • Ectomycorrhizal fungi - potential organic matter decomposers, yet not saprotrophs
  • 2015
  • Ingår i: New Phytologist. - : Wiley. - 1469-8137 .- 0028-646X. ; 205:4, s. 1443-1447
  • Forskningsöversikt (refereegranskat)abstract
    • Although hypothesized for many years, the involvement of ectomycorrhizal fungi in decomposition of soil organic matter remains controversial and has not yet been fully acknowledged as an important factor in the regulation of soil carbon (C) storage. Here, we review recent findings, which support the view that some ectomycorrhizal fungi have the capacity to oxidize organic matter, either by brown-rot' Fenton chemistry or using white-rot' peroxidases. We propose that ectomycorrhizal fungi benefit from organic matter decomposition primarily through increased nitrogen mobilization rather than through release of metabolic C and question the view that ectomycorrhizal fungi may act as facultative saprotrophs. Finally, we discuss how mycorrhizal decomposition may influence organic matter storage in soils and mediate responses of ecosystem C sequestration to environmental changes.
  •  
49.
  • Lyngsie, Gry, et al. (författare)
  • Generation of hydroxyl radicals from reactions between a dimethoxyhydroquinone and iron oxide nanoparticles
  • 2018
  • Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The hydroxyl radical (·OH) is a powerful oxidant that is produced in a wide range of environments via the Fenton reaction (Fe2+ + H2O2 → Fe3+ + ·OH + OH-). The reactants are formed from the reduction of Fe3+ and O2, which may be promoted by organic reductants, such as hydroquinones. The aim of this study was to investigate the extent of ·OH formation in reactions between 2,6-dimethoxyhydroquinone (2,6-DMHQ) and iron oxide nanoparticles. We further compared the reactivities of ferrihydrite and goethite and investigated the effects of the O2 concentration and pH on the generation of ·OH. The main finding was that the reactions between 2,6-DMHQ and iron oxide nanoparticles generated substantial amounts of ·OH under certain conditions via parallel reductive dissolution and catalytic oxidation reactions. The presence of O2 was essential for the catalytic oxidation of 2,6-DMHQ and the generation of H2O2. Moreover, the higher reduction potential of ferrihydrite relative to that of goethite made the former species more susceptible to reductive dissolution, which favored the production of ·OH. The results highlighted the effects of surface charge and ligand competition on the 2,6-DMHQ oxidation processes and showed that the co-adsorption of anions can promote the generation of ·OH.
  •  
50.
  • Malmcrona-Friberg, Karin, et al. (författare)
  • Chemical changes in cell envelope and poly-β-hydroxybutyrate during short term starvation of a marine bacterial isolate
  • 1986
  • Ingår i: Archives of Microbiology. - 0302-8933. ; 144:4, s. 340-345
  • Tidskriftsartikel (refereegranskat)abstract
    • Qualitative and quantitative changes were observed in lipids, poly-β-hydroxybutyrate (PHB), and a cell wall peptidoglycan consitutent in a marine bacterial isolate during starvation for 24 h in an energy and nutrient-free medium. While the amount and composition of the membrane fatty acids fluctuated within the first hours of starvation, the total amount of fatty acids decreased during the starvation period. Furthermore, the ratio of monounsaturated to saturated fatty acids decreased and the proportion of short chain fatty acids increased. In the very early phase of starvation the bacteria contained PHB, which had been accumulated during the growth phase, but after 3 h no PHB was detected. Cells starved for phosphorus showed a different pattern as PHB was initially accumulated and did not decrease until 5 h of starvation. Synthesis of the cell wall amino acid d-alanine was initiated during the first phase of starvation. The effects of these changes on membrane fluidity and uptake of substrates as well as the use of fatty acids and PHB as energy resources during starvation are discussed.
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