| 1. |
- Beckers, Bram, et al.
(författare)
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Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome.
- 2016
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 113:8, s. 2312-2317
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Tidskriftsartikel (refereegranskat)abstract
- Cinnamoyl-CoA reductase (CCR), an enzyme central to the lignin biosynthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. However, silencing of the CCR gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. Here, we evaluated host genotype-dependent effects of field-grown, CCR-down-regulated poplar trees (Populus tremula × Populus alba) on the bacterial rhizosphere microbiome and the endosphere microbiome, namely the microbiota present in roots, stems, and leaves. Plant-associated bacteria were isolated from all plant compartments by selective isolation and enrichment techniques with specific phenolic carbon sources (such as ferulic acid) that are up-regulated in CCR-deficient poplar trees. The bacterial microbiomes present in the endosphere were highly responsive to the CCR-deficient poplar genotype with remarkably different metabolic capacities and associated community structures compared with the WT trees. In contrast, the rhizosphere microbiome of CCR-deficient and WT poplar trees featured highly overlapping bacterial community structures and metabolic capacities. We demonstrate the host genotype modulation of the plant microbiome by minute genetic variations in the plant genome. Hence, these interactions need to be taken into consideration to understand the full consequences of plant metabolic pathway engineering and its relation with the environment and the intended genetic improvement.
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| 2. |
- De Beeck, Michiel Op, et al.
(författare)
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Elucidating fungal decomposition of organic matter at sub-micrometer spatial scales using optical photothermal infrared (O-PTIR) microspectroscopy
- 2024
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Ingår i: Applied and Environmental Microbiology. - 0099-2240. ; 90:2
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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.
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| 3. |
- Eevers, N, et al.
(författare)
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Comparison between cultivated and total bacterial communities associated with Cucurbita pepo using cultivation-dependent techniques and 454 pyrosequencing.
- 2015
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020.
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Tidskriftsartikel (refereegranskat)abstract
- Endophytic bacteria often have beneficial effects on their host plants that can be exploited for bioremediation applications but, according to the literature, only 0.001-1% of all endophytic microbes should be cultivable. This study compared the cultivated endophytic communities of the roots and shoots of Cucurbita pepo with the total endophytic communities as determined by cultivation-dependent techniques and 454 pyrosequencing. The ten most abundant taxa of the total communities aligned well with the cultivated taxa; however, the abundance of these taxa in the two communities differed greatly. Enterobacter showed very low presence in the total communities, whereas they were dominantly present in the cultivated communities. Although Rhizobium dominated in total root and shoot communities, it was poorly cultivable and even then only in growth media containing plant extract. Since endophytes likely contribute to plant-growth promotion, cultivated bacterial strains were tested for their plant-growth promoting capabilities, and the results were correlated with their abundance in the total community. Bacillus and Pseudomonas showed promising results when considering cultivability, abundance in the total community and plant-growth promoting capability. This study demonstrated that, although a limited number of bacterial genera were cultivable, current cultivation-dependent techniques may be sufficient for further isolation and inoculation experiments that aim to improve phytoremediation efficiency.
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| 4. |
- Gu, Kaiyuan, et al.
(författare)
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Effects of topping and non-topping on growth-regulating hormones of flue-cured tobacco (Nicotiana tabacum L.)—a proteomic analysis
- 2023
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Ingår i: Frontiers in Plant Science. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Until now, the mechanism underlying the impact of topping on hormone regulation in tobacco plants remains unclear, and most studies investigating the hormone signaling pathways in plants rely on genes or transcriptional pathways. Methods: This study examines the regulatory mechanisms of hormones in the roots and leaves of tobacco plants with and without topping at the protein level. Results: The results demonstrate that, compared with non-topped plants, topping leads to a decrease in the levels of IAA (auxin), ABA (abscisic acid), and GA (gibberellin) hormones in the leaves, whereas the content of the JA (jasmonic acid) hormone increases. Furthermore, in the roots, topping results in an increase in the levels of IAA, ABA, and JA hormones, along with a decrease in GA content. In the leaves, a total of 258 significantly different proteins were identified before and after topping, with 128 proteins upregulated and 130 proteins downregulated. In the roots, there were 439 proteins with significantly different quantities before and after topping, consisting of 211 upregulated proteins and 228 downregulated proteins. Notably, these proteins were closely associated with the metabolic and biosynthetic pathways of secondary metabolites, as indicated by functional categorization. Conclusions: When integrating the hormone changes and the proteomics results, it is evident that topping leads to increased metabolic activity and enhanced hormone synthesis in the root system. This research provides a theoretical foundation for further investigations into the regulation and signaling mechanisms of hormones at the protein level before and after topping in plants.
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| 5. |
- Jiang, Yonglei, et al.
(författare)
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Rotation cropping and organic fertilizer jointly promote soil health and crop production
- 2022
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Ingår i: Journal of Environmental Management. - : Elsevier BV. - 0301-4797. ; 315
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Tidskriftsartikel (refereegranskat)abstract
- Identifying field management practices to promote crop production, while conserving soil health is essential to maintain long-term food production in a changing world. Also, providing experimental evidence to support the use of traditional agricultural practices is necessary to secure sustainable agriculture. Here, we conducted a long-term 12-year experiment to investigate the impact of different combinations of fertilization type (control, inorganic fertilizer, organic fertilizer) and cropping regimes (continuous cropping and rotation cropping) on the crop (tobacco) production and multiple soil attributes associated with soil health, including proportions of soil-borne pathogens and decomposers, soil microbial diversity, microbial network stability and biomass, nutrient pools and microbial resource limitations. Our long-term experiment supports that the combination of organic fertilizer with rotation cropping increased crop production by at least 40% compared to the other management combinations and improved soil nutrient pools (e.g. the content of soil organic matter), improved the relative proportion of soil decomposers, and promoted bacterial and fungal network stability and biodiversity. Furthermore, this combination treatment relieved microbial resource limitation and reduced the abundance of potential fungal plant pathogens by at least 20% compared to other management combinations. In summary, we provide experimental evidence to support that the combined use of organic fertilization and rotation cropping management can help maintain long-term soil health, crop production, and economic outputs.
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| 6. |
- Krumina, Lelde, et al.
(författare)
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Ectomycorrhizal Fungal Transformation of Dissolved Organic Matter : Consequences for Reductive Iron Oxide Dissolution and Fenton-Based Oxidation of Mineral-Associated Organic Matter
- 2022
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Ingår i: Frontiers in Earth Science. - : Frontiers Media SA. - 2296-6463. ; 10
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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.
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| 7. |
- Li, Jian, et al.
(författare)
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Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland
- 2024
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Ingår i: Environment International. - 0160-4120. ; 187
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Tidskriftsartikel (refereegranskat)abstract
- The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant–microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.
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| 8. |
- Op De Beeck, Michiel, et al.
(författare)
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Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus
- 2018
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Ingår i: New Phytologist. - : Wiley. - 0028-646X. ; 218:1, s. 335-343
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Tidskriftsartikel (refereegranskat)abstract
- Boreal trees rely on their ectomycorrhizal fungal symbionts to acquire growth-limiting nutrients, such as nitrogen (N), which mainly occurs as proteins complexed in soil organic matter (SOM). The mechanisms for liberating this N are unclear as ectomycorrhizal fungi have lost many genes encoding lignocellulose-degrading enzymes present in their saprotrophic ancestors. We hypothesized that hydroxyl radicals (bullOH), produced by the ectomycorrhizal fungus Paxillus involutus during growth on SOM, are involved in liberating organic N. Paxillus involutus was grown for 7 d on N-containing or N-free substrates that represent major organic compounds of SOM. bullOH production, ammonium assimilation, and proteolytic activity were measured daily. bullOH production was strongly induced when P. involutus switched from ammonium to protein as the main N source. Extracellular proteolytic activity was initiated shortly after the oxidation. Oxidized protein substrates induced higher proteolytic activity than unmodified proteins. Dynamic modeling predicted that bullOH production occurs in a burst, regulated mainly by ammonium and ferric iron concentrations. We propose that the production of bullOH and extracellular proteolytic enzymes are regulated by similar nutritional signals. Oxidation works in concert with proteolysis, improving N liberation from proteins in SOM. Organic N mining by ectomycorrhizal fungi has, until now, only been attributed to proteolysis.
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| 9. |
- Op De Beeck, Michiel, et al.
(författare)
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Fungal extracellular polymeric substance matrices – Highly specialized microenvironments that allow fungi to control soil organic matter decomposition reactions
- 2021
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717. ; 159
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Forskningsöversikt (refereegranskat)abstract
- Filamentous fungi play a key role in the terrestrial carbon cycle as they are the primary decomposers of lignocellulose in soil organic matter (SOM). Fungi secrete a wide range of oxidative and hydrolytic enzymes, and generate radicals through extracellular secondary metabolites to decompose SOM. To study fungal decomposition of SOM, the activities of isolated enzymes are typically studied as proxies for the decomposition activity of fungi. However, extracellular enzymes involved in lignocellulose decomposition are often bound to fungal extracellular polymeric substance (EPS) matrices. This association between extracellular enzymes and EPS matrices affects the activities of the enzymes. Moreover, extracellular enzymes and fungal cells are prone to attack by radicals and proteolytic enzymes themselves. Hence, these seemingly incompatible decomposition mechanisms must be regulated in some way in the fungal extracellular space to allow efficient decomposition of SOM, while preventing damage to secreted extracellular enzymes or the fungal cells themselves. We here review studies investigating the associations between fungal extracellular enzymes and EPS matrices and how these associations affect hydrolytic and oxidative reactions involved in SOM decomposition. Based on the knowledge compiled in the current review, we propose that fungal EPS matrices should be viewed as highly dynamic and functional parts of the fungal extracellular decomposition machinery. We also build a conceptual illustration that describes how the molecular composition and structure of fungal EPS matrices ensure that extracellular decomposition reactions only proceed at the right time and in the right place.
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| 10. |
- Op De Beeck, Michiel, et al.
(författare)
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Regulation of fungal decomposition at single-cell level
- 2020
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 14:4, s. 896-905
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Tidskriftsartikel (refereegranskat)abstract
- Filamentous fungi play a key role as decomposers in Earth’s nutrient cycles. In soils, substrates are heterogeneously distributed in microenvironments. Hence, individual hyphae of a mycelium may experience very different environmental conditions simultaneously. In the current work, we investigated how fungi cope with local environmental variations at single-cell level. We developed a method based on infrared spectroscopy that allows the direct, in-situ chemical imaging of the decomposition activity of individual hyphal tips. Colonies of the ectomycorrhizal Basidiomycete Paxillus involutus were grown on liquid media, while parts of colonies were allowed to colonize lignin patches. Oxidative decomposition of lignin by individual hyphae growing under different conditions was followed for a period of seven days. We identified two sub-populations of hyphal tips: one with low decomposition activity and one with much higher activity. Active cells secreted more extracellular polymeric substances and oxidized lignin more strongly. The ratio of active to inactive hyphae strongly depended on the environmental conditions in lignin patches, but was further mediated by the decomposition activity of entire mycelia. Phenotypic heterogeneity occurring between genetically identical hyphal tips may be an important strategy for filamentous fungi to cope with heterogeneous and constantly changing soil environments.
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