| 1. |
- Unterseher, Martin, et al.
(författare)
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Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition
- 2018
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Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 17:4
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Tidskriftsartikel (refereegranskat)abstract
- Multiple biotic and abiotic parameters influence the dynamics of individual fungal species and entire communities. Major drivers for tropical plant endophytes are undoubtedly seasonality, local habitat conditions and biogeography. However, host specialization and tissue preferences also contribute to the structuring of endophytic mycobiomes. To elucidate such specializations and preferences, we sampled two commercially important, unrelated plant species, Amorphophallus albispathus and Camellia sinensis (tea plant) simultaneously at close proximity. The mycobiomes of different tissue types were assessed with high-throughput amplicon sequencing of the internal transcribed spacer DNA region. Both plants hosted different fungal communities and varied in α- and β-diversity, despite their neighboring occurrence. However, the fungal assemblages of Amorphophallus leaflets shared taxa with the mycobiomes of tea leaves, thereby suggesting common driving forces for leaf-inhabiting fungi irrespective of host plant identity. The mycobiome composition and diversity of tea leaves was clearly driven by leaf age. We suggest that the very youngest tea leaves are colonized by stochastic processes, while mycobiomes of old leaves are rather similar as the result of progressive succession. The biodiversity of fungi associated with A. albispathus was characterized by a large number of unclassified OTUs (at genus and species level) and by tissue-specific composition.This study is the first cultivation-independent high-throughput assessment of fungal biodiversity of an Amorphophallus species, and additionally expands the knowledge base on fungi associated with tea plants.
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| 2. |
- Bag, Pushan, 1993-
(författare)
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How could Christmas trees remain evergreen? : photosynthetic acclimation of Scots pine and Norway spruce needles during winter
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plants and other green organisms harvest sunlight by green chlorophyll pigments and covertit to chemical energy (sugars) and oxygen in a process called photosynthesis providing the foundation for life on Earth. Although it is unanimously believed that oceanic phytoplanktons are the main contributors to the global photosynthesis, the contribution of coniferous boreal forests distributed across vast regions of the northern hemisphere cannot be undermined. Hence boreal forests account signifificantly for social, economical and environmental sustainability. Not only do conifers thrive in the tundra regions with extreme climate, but they also maintain their needles green over the boreal winter. A question remains; what makes them so resilient? In this respect, we aimed to understand the remarkable winter adaptation strategies in two dominant boreal coniferous species,i.e., Pinus sylvestris and Picea abies. First, we mapped the transcriptional landscape in Norway spruce (Picea abies) needles over the annual cycle. Transcriptional changes in the nascent needles reflflected a sequence of developmental processes and active vegetative growth during early summer and summer. Later after maturation, transcriptome reflflected activated defense against biotic factors and acclimationin response to abiotic environmental cues such as freezing temperatures during winter. Secondly, by monitoring the photosynthetic performance of Scot pine needles, we found that the trees face extreme stress during the early spring (Feb-Mar) when sub-zero temperatures are accompanied by high solar radiation. At this time, drastic changes occur in the thylakoid membranes of the chloroplast that allows the mixing of photosystem I and photosystem II that typically remain laterally segregated. This triggers direct energy transfer from PSII to PSI and thus protects PSII from damage. Furthermore, we found that this loss of lateral segregation may be a consequence of triple phosphorylationof Lhcb1 (Light harvesting complex1 of photosystem II). The structural changes in thylakoid membranes also lead to changes inthe thylakoid macro domain organisationand pigment protein composition. Furthermore, we discovered that while PSII is protected by direct energy transfer, the protection of PSI is provided through photoreduction of oxygen by flavodiiron proteins, which in turn allows P700 to stay in an oxidised state necessary for direct energy transfer. These coordinated cascades of changes concomitantly protect both PSI and PSII to maintain the needles green over the winter.
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| 3. |
- Siddique, Abu Bakar, First research engineer, et al.
(författare)
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What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions
- 2017
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 20, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- Comparative simultaneous studies of environmental high-throughput sequencing (HTS) and cultivation of plant-associated fungi have rarely been conducted in the past years. For the present contribution, HTS and extinction culturing were applied for the same leaf samples of European beech (Fagus sylvatica) in order to trace both “real” environmental drivers as well as method-dependent signals of the observed mycobiomes. Both approaches resulted in non-overlapping community composition and pronounced differences in taxonomic classification and trophic stages. However, both methods revealed similar correlations of the fungal communities with local environmental conditions. Our results indicate undeniable advantages of HTS over cultivation in terms of revealing a good representation of the major functional guilds, rare taxa and biodiversity signals of leaf-inhabiting fungi. On the other hand our results demonstrate that the immense body of literature about cultivable endophytic fungi can and should be used for the interpretation of community signals and environmental correlations obtained from HTS studies and that cultivation studies should be continued at the highest standards, e.g. when sequencing facilities are not available or if such surveys are expanded into functional aspects with experiments on living isolates.
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| 4. |
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| 5. |
- Wedin, Mats, et al.
(författare)
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Slippery when wet: Phylogeny and character evolution in the gelatinous cyanobacterial lichens (Peltigerales, Ascomycetes)
- 2009
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Ingår i: Molecular Phylogenetics and Evolution. - San Diego : Elsevier BV. - 1055-7903 .- 1095-9513. ; 53:3, s. 862-871
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Tidskriftsartikel (refereegranskat)abstract
- Many lichen fungi form symbioses with filamentous Nostoc cyanobacteria, which cause the lichen toswell and become extremely gelatinous when moist. Within the Lecanoromycetes, such gelatinous lichens are today mainly classified in the Collemataceae (Peltigerales, Ascomycota). We performed Bayesian MCMC, maximum likelihood, and maximum parsimony analyses of three independent markers(mtSSU rDNA, nuLSU rDNA, and RPB1), to improve our understanding of the phylogeny and classification in the Peltigerales, as well as the evolution of morphological characters that have been used for classification purposes in this group. The Collemataceae and the non-gelatinous Pannariaceae are paraphyleticbut can be re-circumscribed as monophyletic if Leciophysma, Physma, Ramalodium and Staurolemma are transferred to the Pannariaceae. The gelatinous taxa transferred to the Pannariaceae deviate from other Collemataceae in having simple ascospores, and several also have a ring-shaped exciple as in other Pannariaceae, rather than the disc-shaped exciple found in the typical Collemataceae. Both Collema and Leptogium are non-monophyletic. The re-circumscribed Collemataceae shares a distinct ascus type withthe sister group Placynthiaceae and the Coccocarpiaceae, whereas Pannariaceae includes a variety of structures. All Pannariaceae have one-celled ascospores, whereas all Collemataceae have two- or multi-celled spores. Reconstructions of the number of character state transformations in exciple structure, thallus gelatinosity, and ascus apex structure indicate that the number of transformations is distinctly higher than the minimum possible. Most state transformations in the exciple took place from aring-shaped to a disc-shaped exciple. Depending on the reconstruction method, most or all transformationsin thallus structure took place from a non-gelatinous to a gelatinous thallus. Gains and losses of internal structures in the ascus apex account for all or a vast majority of the number of transformations in the ascus, whereas direct transformations between asci with internal structures appear to have been rare.
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| 6. |
- Siddique, Abu Bakar, First research engineer, et al.
(författare)
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Optimization of Protocol for Construction of Fungal ITS Amplicon Library for High-Throughput Illumina Sequencing to Study the Mycobiome of Aspen Leaves
- 2022
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Ingår i: Applied Sciences. - : MDPI. - 2076-3417. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.
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| 7. |
- Bolnick, Daniel, et al.
(författare)
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Comparative support for the niche variation hypothesis that more generalized populations also are more heterogeneous
- 2007
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 104:24, s. 10075-10079
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Tidskriftsartikel (refereegranskat)abstract
- There is extensive evidence that some species of ecological generalists, which use a wide diversity of resources, are in fact heterogeneous collections of relatively specialized individuals. This within-population variation, or "individual specialization," is a key requirement for frequency-dependent interactions that may drive a variety of types of evolutionary diversification and may influence the population dynamics and ecological interactions of species. Consequently, it is important to understand when individual specialization is likely to be strong or weak. The niche variation hypothesis (NVH) suggests that populations tend to become more generalized when they are released from interspecific competition. This niche expansion was proposed to arise via increased variation among individuals rather than increased individual niche breadth. Consequently, we expect ecological generalists to exhibit stronger individual specialization, but this correlation has been repeatedly rejected by empiricists. The drawback with previous empirical tests of the NVH is that they use morphological variation as a proxy for niche variation, ignoring the role of behavior and complex phenotype-function relationships. Here, we used diet data to directly estimate niche variation among individuals. Consistent with the NVH, we show that more generalized populations also exhibit more niche variation. This trend is quite general, appearing in all five case studies examined: three-spine stickleback, Eurasian perch, Anolis lizards, intertidal gastropods, and a community of neotropical frogs. Our results suggest that generalist populations may tend to be more ecologically variable. Whether this translates into greater genetic variation, evolvability, or ecological stability remains to be determined.
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| 8. |
- Larsson, Anders, et al.
(författare)
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Identification of the brominated flame retardant 1,2-dibromo-4-(1,2-dibromoethyl)cyclohexane as an androgen agonist
- 2006
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Ingår i: Journal of medicinal chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 49:25, s. 7366-7372
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Tidskriftsartikel (refereegranskat)abstract
- To investigate androgen receptor (AR) activation by exogenous compounds, we used a combination of experimental analysis and theoretical modeling to compare a set of brominated flame retardants (BFRs) to dihydrotestosterone (DHT) with regard to ligand docking, AR binding, and AR activation in human hepatocellular liver carcinoma cells, as well as interacting energy analysis. Modeling of receptor docking was found to be a useful first step in predicting the potential to translocate to the ligand pocket of the receptor, and the computed interaction energy was found to correlate with the observed binding affinity. Flexible alignment studies of the BFR compounds demonstrated that 1,2-dibromo-4-(1,2-dibromoethyl)cyclohexane (BCH) closely overlap DHT. Combining the theoretical modeling with in vitro ligand-binding and receptor-activation assays, we show that BCH binds to and activates the human AR. The remaining BFRs did not successfully interact with the ligand pocket, were not able to replace a synthetic androgen from the receptor, and failed to activate the receptor.
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| 9. |
- Mobley, Kenyon B., et al.
(författare)
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The effect of maternal body size on embryo survivorship in the broods of pregnant male pipefish
- 2011
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Ingår i: Behavioral Ecology and Sociobiology. - : Springer Science and Business Media LLC. - 0340-5443 .- 1432-0762. ; 65:6, s. 1169-1177
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Tidskriftsartikel (refereegranskat)abstract
- The occurrence of male pregnancy in the family Syngnathidae (seahorses, pipefishes, and sea dragons) provides an exceptionally fertile system in which to investigate issues related to the evolution of parental care. Here, we take advantage of this unique reproductive system to study the influence of maternal body size on embryo survivorship in the brood pouches of pregnant males of the broad-nosed pipefish, Syngnathus typhle. Males were mated with either two large females, two small females, a large then a small female, or a small then a large female. Our results show that offspring survivorship depends on an interaction between female body size and the number of eggs transferred by the female. Eggs of larger females deposited in large numbers are more likely to result in viable offspring than eggs of smaller females laid in large numbers. However, when females deposited smaller numbers of eggs, the eggs from smaller females were more likely to produce viable offspring compared to those from larger females. We found no evidence that this result was based on mating order, the relative sizes of competing females, or egg characteristics such as dry weight of eggs. Additionally, male body size did not significantly influence the survivorship of offspring during brooding. Our results suggest that the factors underlying offspring survivorship in pipefish may be more complex than previously believed, with multiple factors interacting to determine the fitness of individual offspring within the broods of pregnant males.
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| 10. |
- Unterseher, Martin, et al.
(författare)
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Diversity and Composition of the Leaf Mycobiome of Beech (Fagus sylvatica) Are Affected by Local Habitat Conditions and Leaf Biochemistry
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- Comparative investigations of plant-associated fungal communities (mycobiomes) in distinct habitats and under distinct climate regimes have been rarely conducted in the past. Nowadays, high-throughput sequencing allows routine examination of mycobiome responses to environmental changes and results at an unprecedented level of detail. In the present study, we analysed Illumina-generated fungal ITS1 sequences from European beech (Fagus sylvatica) originating from natural habitats at two different altitudes in the German Alps and from a managed tree nursery in northern Germany. In general, leaf-inhabiting mycobiome diversity and composition correlated significantly with the origin of the trees. Under natural condition the mycobiome was more diverse at lower than at higher elevation, whereas fungal diversity was lowest in the artificial habitat of the tree nursery. We further identified significant correlation of leaf chlorophylls and flavonoids with both habitat parameters and mycobiome biodiversity. The present results clearly point towards a pronounced importance of local stand conditions for the structure of beech leaf mycobiomes and for a close interrelation of phyllosphere fungi and leaf physiology.
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