| 1. |
- Bakys, Remigijus, et al.
(författare)
-
Investigations concerning the role of Chalara fraxinea in declining Fraxinus excelsior
- 2009
-
Ingår i: Plant Pathology. - : Wiley. - 0032-0862 .- 1365-3059. ; 58, s. 284-292
-
Tidskriftsartikel (refereegranskat)abstract
- A study was carried out to clarify the role of the fungus Chalara fraxinea in decline of Fraxinus excelsior, which is observed on a large scale in central and northern Europe with high incidence of tree mortality. The aims of this work were: (i) to check for the presence of C. fraxinea in various tissues of declining F. excelsior by agar culture isolations and by direct analysis of plant tissues using molecular techniques (DNA extraction, ITS-PCR, cloning, ITS sequencing and T-RFLP); (ii) to study fungal communities inhabiting tissues with symptoms; and (iii) to test the pathogenicity of C. fraxinea to F. excelsior. Chalara fraxinea was isolated from 93% of stem cankers, 91% of necrotic leaf stalks, 27-28% of bark wounds and 30% of visually healthy leaf stalks. Molecular analyses of necrotic leaves, leaf stalks and bark revealed the presence of 25 different fungal taxa, 14 of which were detected in all three types of tissue sample. Chalara fraxinea was the second most common species (61% of samples), and only Cryptococcus foliicola occurred more often (70%). All eight of the tested C. fraxinea isolates induced necroses in bark and cambium on each of 86 inoculated trees, and all controls remained healthy. Average length of necroses caused by different C. fraxinea strains varied from 4.2 to 8.9 cm, but the differences were statistically insignificant. Instead, differences in resistance of individual trees to C. fraxinea were observed.
|
|
| 2. |
- Bakys, Remigijus, et al.
(författare)
-
Root rot, associated fungi and their impact on health condition of declining Fraxinus excelsior stands in Lithuania
- 2011
-
Ingår i: Scandinavian Journal of Forest Research. - : Informa UK Limited. - 0282-7581 .- 1651-1891. ; 26, s. 128-135
-
Tidskriftsartikel (refereegranskat)abstract
- Dieback of Fraxinus excelsior L. associated with Chalara fraxinea is observed in Europe, and in some areas dying trees exhibit symptoms of root and butt rot. Our study was conducted (1) to estimate the impact of the rot on F. excelsior dieback severity; (2) to identify fungi colonizing roots of dieback-affected trees; (3) to check their pathogenicity to F. excelsior; and (4) to estimate sprouting incidence and sprout health condition in relation to presence/absence of rot. The extent of rot was measured in 33 trees with different dieback intensity, 150 fungal isolations were attempted from roots of 50 trees, 26 fungi were tested for pathogenicity to 286 saplings, and sprouting was evaluated for 328 stumps on three clear-felled sites. Root rot was mainly caused by Armillaria cepistipes, and the extent of rot correlated positively with dieback severity although it played a secondary role in tree decline. Four years after tree felling, root rot had a negative impact on sprouting frequency, yet rot did not enter sprouts from stumps, and when experimentally inoculated, fungi associated with root rot in mature ash had no visible impact on tree vigor, showing that after formation of sprouts, rot does not affect the subsequent phytosanitary condition. Sprouts on investigated sites exhibited Chalara dieback symptoms on leaves and bark irrespectively of presence/absence of rot, indicating that vigorous natural regeneration of F. excelsior in dieback-affected areas could not be expected.
|
|
| 3. |
- Barbi, Florian, et al.
(författare)
-
Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers
- 2020
-
Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 22, s. 1089-1103
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 4. |
- Bengtsson, Stina, et al.
(författare)
-
Detection of Chalara fraxinea from tissue of Fraxinus excelsior using species-specific ITS primers
- 2010
-
Ingår i: Forest Pathology. - : Wiley. - 1437-4781 .- 1439-0329. ; 40, s. 111-115
-
Tidskriftsartikel (refereegranskat)abstract
- P>Chalara fraxinea (teleomorph: Hymenoscyphus albidus) is known as a serious pathogen of Fraxinus excelsior, causing massive dieback of trees in Europe. The fungus is able to cause latent infections, and has been previously detected as an endophyte in asymptomatic tissues. Chalara fraxinea is a slow grower in culture, and is thus likely to be overgrown by faster growing fungi whenever pure culture isolations are being attempted. This study reports species-specific ITS primers allowing fast and reliable detection of the pathogen directly from infected tissues of F. excelsior.
|
|
| 5. |
- Boberg, Johanna, et al.
(författare)
-
Decomposing capacity of fungi commonly detected in Pinus sylvestris needle litter
- 2011
-
Ingår i: Fungal Ecology. - : Elsevier BV. - 1754-5048 .- 1878-0083. ; 4, s. 110-114
-
Tidskriftsartikel (refereegranskat)abstract
- A major part of the fungal community in coniferous litter consists of fungi whose taxonomic position and ecology are unknown. Here, nine isolates from within commonly occurring phylogenetic groups were tested for their ability to decompose Pinus sylvestris needles. In a 1-yr long incubation study, needle mass loss as well as changes in cellulose and lignin content were determined and compared to those caused by two litter basidiomycetes (Marasmius androsaceus and Mycena epipterygia) with recognized ability to decompose needles. A basidiomycetous Clavulina/Sistotrema strain appeared to be cellulolytic but not ligninolytic. Chalara longipes and three other strains within Helotiales also decomposed cellulose but not lignin, whereas Mollisia cinerea (also Helotiales) and two Dothideomycetes - Sydowia polyspora and a Mytilinidion sp., seemed unable to cause significant mass loss of cellulose. Lophodermium pinastri (Rhytismatales) readily decomposed cellulose, and also caused considerable loss of lignin. (C) 2010 Elsevier Ltd and The British Mycological Society. All rights reserved.
|
|
| 6. |
- Broberg, Martin, et al.
(författare)
-
Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales)
- 2021
-
Ingår i: Evolutionary applications. - : Wiley. - 1752-4571. ; 14, s. 476-497
-
Tidskriftsartikel (refereegranskat)abstract
- Various strains of the mycoparasitic fungal speciesClonostachys roseaare used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy ofC. roseain biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction betweenC. roseaand plant pathogenic fungi. Here, we determined the genome sequences of 11Clonostachysstrains, representing five species inClonostachyssubgenusBionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p <= .05) in theBionectriasubgenus lineage. This was accompanied with gene copy number increases (p <= .05) in ATP-binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. MostClonostachysspecies were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose-methanol-choline oxidoreductases and additional carbohydrate-active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of theC. roseagenome included expansions (p <= .05) of the ABC-B4 multidrug resistance transporters, the ABC-C5 multidrug resistance-related transporters and the 2.A.1.3 drug:H + antiporter-2 MFS drug resistance transporters. The ABC-G1 pleiotropic drug resistance transporter geneabcG6inC. roseawas induced (p <= .009) by exposure to the antifungalFusariummycotoxin zearalenone (1121-fold) and various fungicides. Deletion ofabcG6resulted in mutants with reduced (p < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites inClonostachyssubgenusBionectria.
|
|
| 7. |
- Broberg, Martin, et al.
(författare)
-
Out in the Cold: Identification of Genomic Regions Associated With Cold Tolerance in the Biocontrol Fungus Clonostachys rosea Through Genome-Wide Association Mapping
- 2018
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- There is an increasing importance for using biocontrol agents in combating plant diseases sustainably and in the long term. As large scale genomic sequencing becomes economically viable, the impact of single nucleotide polymorphisms (SNPs) on biocontrol-associated phenotypes can be easily studied across entire genomes of fungal populations. Here, we improved a previously reported genome assembly of the biocontrol fungus Clonostachys rosea strain IK726 using the PacBio sequencing platform, which resulted in a total genome size of 70.7 Mbp and 21,246 predicted genes. We further performed whole-genome re-sequencing of 52 additional C. rosea strains isolated globally using Illumina sequencing technology, in order to perform genome-wide association studies in conditions relevant for biocontrol activity. One such condition is the ability to grow at lower temperatures commonly encountered in cryic or frigid soils in temperate regions, as these will be prevalent for protecting growing crops in temperate climates. Growth rates at 10 degrees C on potato dextrose agar of the 53 sequenced strains of C. rosea were measured and ranged between 0.066 and 0.413 mm/day. Performing a genome wide association study, a total of 1,478 SNP markers were significantly associated with the trait and located in 227 scaffolds, within or close to (<1000 bp distance) 265 different genes. The predicted gene products included several chaperone proteins, membrane transporters, lipases, and proteins involved in chitin metabolism with possible roles in cold tolerance. The data reported in this study provides a foundation for future investigations into the genetic basis for cold tolerance in fungi, with important implications for biocontrol.
|
|
| 8. |
- Castaño Soler, Carles, et al.
(författare)
-
Optimized metabarcoding with Pacific biosciences enables semi-quantitative analysis of fungal communities
- 2020
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 228, s. 1149-1158
-
Tidskriftsartikel (refereegranskat)abstract
- Recent studies have questioned the use of high-throughput sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region to derive a semi-quantitative representation of fungal community composition. However, comprehensive studies that quantify biases occurring during PCR and sequencing of ITS amplicons are still lacking. We used artificially assembled communities consisting of 10 ITS-like fragments of varying lengths and guanine-cytosine (GC) contents to evaluate and quantify biases during PCR and sequencing with Illumina MiSeq, PacBio RS II and PacBio Sequel I technologies. Fragment length variation was the main source of bias in observed community composition relative to the template, with longer fragments generally being under-represented for all sequencing platforms. This bias was three times higher for Illumina MiSeq than for PacBio RS II and Sequel I. All 10 fragments in the artificial community were recovered when sequenced with PacBio technologies, whereas the three longest fragments (> 447 bases) were lost when sequenced with Illumina MiSeq. Fragment length bias also increased linearly with increasing number of PCR cycles but could be mitigated by optimization of the PCR setup. No significant biases related to GC content were observed. Despite lower sequencing output, PacBio sequencing was better able to reflect the community composition of the template than Illumina MiSeq sequencing.
|
|
| 9. |
- Chaudhary, Rajiv, et al.
(författare)
-
Marker-Trait Associations for Tolerance to Ash Dieback in Common Ash (Fraxinus excelsior L.)
- 2020
-
Ingår i: Forests. - : MDPI. - 1999-4907. ; 11:10
-
Tidskriftsartikel (refereegranskat)abstract
- Common ash (Fraxinus excelsior L.) is a tree species of significant ecological and economic importance that has suffered a devastating decline since the 1990s in Europe. Native ash species are being threatened by the alien invasive fungus Hymenoscyphus fraxineus, which causes ash dieback. The main goal of the study was to develop markers for traits related to tolerance to ash dieback and to investigate whether genotypes selected for tolerance were genetically different from susceptible wild populations. We phenotyped 326 ash trees from Sweden for disease severity and genotyped them using 63 amplicon-derived single-nucleotide polymorphism (SNP) markers derived from genes in 40 scaffolds spanning 8 MB in total, which represents approximately 1% of the ash genome. We used a mixed linear model to test for an association between genotypic variation at these loci and disease severity of ash. In total, two SNPs were found to have significant associations. One non-synonymous SNP associated with the disease severity of ash was found in a gene predicted to encode a subtilisin-related peptidase S8/S53 domain. A second marginally significant marker was associated with an LRR gene. Our results demonstrate an inexpensive time-effective method for generating genomic data that could have potential for use in future tree breeding programs and provide information for marker-assisted selection. Our study also showed a low differentiation between genotypes selected for disease tolerance and the wild population of ash representing a range of susceptibilities to ash dieback, indicating opportunities for further selection without significantly losing genetic diversity in the ash population.
|
|
| 10. |
- Clemmensen, Karina, et al.
(författare)
-
Sample preparation for fungal community analysis by high-throughput sequencing of barcode amplicons
- 2023
-
Ingår i: Microbial Environmental Genomics (MEG) ; second edition. - New York, NY : Springer US. - 9781071628706 ; :2605, s. 37-64
-
Bokkapitel (refereegranskat)abstract
- Fungal species participate in vast numbers of processes in the landscape around us. However, their cryptic mycelial growth, inside various substrates and in highly diverse species assemblages, has been a major obstacle to thorough analysis of fungal communities, hampering exhaustive description of the fungal kingdom. Technological developments allowing rapid, high-throughput sequencing of mixed communities from many samples at once are currently having a tremendous impact in fungal community ecology. Universal DNA extraction followed by amplification and sequencing of fungal species-level barcodes such as the nuclear internal transcribed spacer (ITS) region now enables identification and relative quantification of fungal community members across well-replicated experimental settings. Here, we present the sample preparation procedure presently used in our laboratory for fungal community analysis by high-throughput sequencing of amplified ITS2 markers. We focus on the procedure optimized for studies of total fungal communities in humus-rich soils, wood, and litter. However, this procedure can be applied to other sample types and markers. We focus on the laboratory-based part of sample preparation, i.e., the procedure from the point where samples enter the laboratory until amplicons are submitted for sequencing. Our procedure comprises four main parts: (1) universal DNA extraction, (2) optimization of PCR conditions, (3) production of tagged ITS amplicons, and (4) preparation of the multiplexed amplicon pool to be sequenced. The presented procedure is independent of the specific highthroughput sequencing technology used, which makes it highly versatile.
|
|
