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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Ma, Jin-Ze, et al.
(författare)
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Environmental Together With Interspecific Interactions Determine Bryophyte Distribution in a Protected Mire of Northeast China
- 2020
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Ingår i: Frontiers in Earth Science. - : Frontiers Media SA. - 2296-6463. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Question: What environmental variables and plant–plant interactions affect mire bryophyte distribution and does the surrounding landscape with human disturbance play a role in the mire bryophyte distribution?Location: Jinchuan mire, Northeast China.Methods: We studied the spatial distribution of bryophytes in 100 1 × 1 m quadrats in the mire. Spatial variables were simulated by analysis of the distance-based Moran’s eigenvector maps (dbMEM). Variation partitioning analysis was used to reveal the relative contribution of spatial and environmental variables to bryophytes. The relationship between environmental variables and bryophytes was tested by redundancy analysis (RDA). We used co-occurrence and niche overlap models to detect interactions among bryophytes. We also studied the influence of the surrounding landscape on the distribution of bryophytes in relation to water chemistry.Results: The eight bryophytes occupying part of the mire had both a general distribution trend and a local spatial structure. Over 40% of the total variation in cover among bryophytes could be explained by spatial and environmental variables. In this fraction, the environmental variables explained 29.7% of the variation, of which only 4.5% was not spatially structured. RDA showed the contribution of dwarf shrub cover (SC), Na, and P to the bryophyte distribution was relatively large. Concentration of Na and SC decreased gradually from north to south, and contributed most to the variation in species composition along the first axis. The concentrations of P decreased from east to west, and contributed along the second axis. All the bryophyte species were spatially isolated but with large niche overlaps, indicating that the bryophyte community was structured by interspecific competition.Conclusion: Sodium mainly originating from the volcanic hill and P from the paddy fields were the main environmental factors affecting the bryophyte distribution. Concentrations of Na and P showed spatial structure, and resulted in induced spatial dependence (ISD) playing a major role in the spatial structure of the bryophyte community. Dwarf shrubs affected by nutrient distribution in the mire significantly influenced the bryophyte distribution in the mire. We conclude that the surrounding ecosystems had important influence on bryophyte distribution via nutrient influx. Furthermore, competitive interactions exacerbated the spatial separation of bryophytes.
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| 4. |
- Graf, Daniel, et al.
(författare)
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Assembly of root-associated N₂O-reducing communities of annual crops is governed by selection for nosZ Glade I over Glade II
- 2022
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 98
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Tidskriftsartikel (refereegranskat)abstract
- The rhizosphere is a hotspot for denitrification. The nitrous oxide (N₂O) reductase among denitrifiers and nondenitrifying N₂O reducers is the only known N₂O sink in the biosphere. We hypothesized that the composition of root-associated N₂O-reducing communities when establishing on annual crops depend on soil type and plant species, but that assembly processes are independent of these factors and differ between nosZ clades I and II. Using a pot experiment with barley and sunflower and two soils, we analyzed the abundance, composition, and diversity of soil and root-associated N₂O reducing communities by qPCR and amplicon sequencing of nosZ. Clade I was more abundant on roots compared to soil, while clade II showed the opposite. In barley, this pattern coincided with N₂O availability, determined as potential N₂O production rates, but for sunflower no N₂O production was detected in the root compartment. Root and soil nosZ communities differed in composition and phylogeny-based community analyses indicated that assembly of root-associated N₂O reducers was driven by the interaction between plant and soil type, with inferred competition being more influential than habitat selection. Selection between clades I and II in the root/soil interface is suggested, which may have functional consequences since most clade I microorganisms can produce N₂O.
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| 5. |
- Graf, Daniel, et al.
(författare)
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Lucerne (Medicago sativa) alters N2O-reducing communities associated with cocksfoot (Dactylis glomerata) roots and promotes N2O production in intercropping in a greenhouse experiment
- 2019
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 137
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Tidskriftsartikel (refereegranskat)abstract
- Lower emissions of the greenhouse gas nitrous oxide (N2O) are generally observed from intercropped compared to sole cropped systems. This could be due to better N-use efficiency, but differences in microbial communities establishing in the rhizosphere may also play a role as the only known biological sink for N2O is its reduction to nitrogen gas (N-2) by bacteria and archaea that possess the nosZ gene encoding the N2O reductase. Nitrous oxide reducing communities can be divided into two clades, I and II, and their relative abundance and diversity may have important consequences for N2O emissions. Here, we examine how intercropping with a legume (Medicago sativa, "lucerne") and a grass (Dactylis glomerata, "cocksfoot") species, compared to sole cropping of each species, affects the N2O emission potential, and the structure and abundance of root-associated N2O-reducing microbial communities. In a rhizobox experiment, we show that intercropping resulted in higher total shoot biomass compared to sole cropping. Further, N2O production rates were significantly higher in intercropped cocksfoot roots compared to sole cropping of either species. This coincided with lower abundances of nosZ Glade II communities in intercropped compared to sole cropped cocksfoot roots, suggesting that these organisms likely act as a N2O sink. Phylogenetic placement of sequencing reads placed root-associated nosZ Glade II reads close to Ignavibacteria and Opitutaceae, which harbour non-denitrifying N2O reducers with the genetic capacity to also perform dissimilatory nitrate reduction to ammonium (DNRA). We observed a shift in the composition of the cocksfoot root-associated nosZI communities towards incomplete denitrifiers terminating with N2O in intercropped roots. Overall, we hypothesize that such alterations of plant-microbe and/or microbe-microbe interactions contributed to the higher potential N2O emission rate observed in intercropped cocksfoot roots. Understanding the nature of these interactions would represent an important step forward for the design of management practices that minimize N2O emissions.
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| 6. |
- Graf, Daniel, et al.
(författare)
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Soil type overrides plant effect on genetic and enzymatic N2O production potential in arable soils
- 2016
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Ingår i: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 100, s. 125-128
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Tidskriftsartikel (refereegranskat)abstract
- Nitrous oxide (N2O) is a potent greenhouse gas mainly produced by incomplete denitrification in agricultural soils. The rhizosphere is a hot spot for denitrification and this study aimed to discern the relative importance of soil type and crop on the genetic N2O production and reduction potential in soil and root associated communities in relation to denitrification activity. Based on a pot experiment with two agricultural soils planted with barley or sunflower, we showed that the effect of soil type overrode that of crop on both genetic and enzymatic potential. We also demonstrate niche differentiation between the nitrous oxide reductase genes nosZI and nosZII, with clade I dominating in the root-associated community and clade II in the soil. (C) 2016 Elsevier Ltd. All rights reserved.
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| 7. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 8. |
- Zhao, Enid Ming, et al.
(författare)
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Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata
- 2017
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Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 119, s. 260-266
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Tidskriftsartikel (refereegranskat)abstract
- The effect of intercropping on the genetic potential for N-cycle pathways promoting either retention or loss of N by the microbial communities associated to the roots or present in the bulk soil for two forage crops was studied in a greenhouse experiment. Medicago sativa ('lucerne') and Dactylis glomerata ('cocksfoot') were grown as sole crops or intercropped in soils with or without addition of biogas digestate to also evaluate fertilizer effects. Eight genes involved in inorganic N-cycling were quantified using real-time PCR to determine the genetic potential for different N-cycling pathways. Both plant species and intercropping affected the abundance of root-associated microbial-derived genes involved in N-cycling processes, while there was no effect of amendment with biogas digestate. The genetic potential for the various pathways differed between bulk soil and roots, as well as between the roots of the two plant species, suggesting that organisms involved in different N-cycling processes were favored in different compartments in the soil-root environment. Ammonia oxidizers involved in nitrification, a pathway resulting in N-leaching, dominated in soil whereas those related to N-2 fixation and gaseous N losses (denitrification) were more abundant on roots. We also observed niche differentiation between the two major groups of organisms with the capacity to reduce N2O in the root- and soil compartment. Legume-grass intercropping resulted in a decreasing trend for several root- associated functional communities. More specifically, the legume exerted an effect on the N-cycling communities on the roots of both the legume and grass species, which suggests altered plant-microbial or microbial-microbial interactions during intercropping.
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| 9. |
- Zhao, Enid Ming
(författare)
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Nitrogen cycling communities associated to roots of arable crops in relation to management : plant, intercropping and soil effects
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Management of terrestrial nitrogen (N) has been identified as a key challenge in the implementation of sustainable agricultural practices. Transformations of inorganic N are mainly performed by microbial functional guilds that regulate the retention or loss of N. Soil management may affect the diversity, composition, and functioning of N-cycling microbial communities. The aim was to define the influence of soil properties, crops and intercropping on root- and soil-associated N-cycling communities with a special focus on the genetic and enzymatic potential for denitrification and nitrous oxide (N₂O) reduction. A greenhouse experiment comparing intercropped cocksfoot and lucerne with sole cropping practices showed that plant species and intercropping significantly affected the abundances of root associated communities that drive the retention or loss of N, suggesting altered plant-microbial and/or microbial-microbial interactions. Addition of biogas digestate as fertilizer did not alter the intercropping effects. A higher N₂O production rate was found in root-associated microbial communities in cocksfoot during intercropping, which coincided with decreased genetic potential for N₂O reduction by organisms within nosZ clade II compared to sole cropped cocksfoot. Sequencing revealed that these N₂O reducers were related to Ignavibacteria, which have a truncated denitrification pathway that lacks the genetic capacity to produce N₂O. Soil type also had a strong influence on root-associated N-cycling communities. In a full-factorial experiment with two soil types and two different crops (barley and sunflower), soil type overrode crop effects regarding both genetic and enzymatic potential for denitrification. Thus, soil physical and chemical properties rather than plant species determine the denitrification and N₂O production rates of the root-associated communities. The genetic potential for the various N-cycling communities differed between bulk soil and roots, indicating that N-cycling functional organisms were favored in different compartments in the soil-root environment. The N₂O reducing organisms carrying nosZI were shown to have an affinity to plant roots, whereas those with nosZII prefer the bulk soil thus indicating a possible niche differentiation between the two clades.
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