| 1. |
- Santangelo, James S., et al.
(författare)
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Global urban environmental change drives adaptation in white clover
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375
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Tidskriftsartikel (refereegranskat)abstract
- Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural dines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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| 2. |
- Abdelfattah, Ahmed, et al.
(författare)
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Evidence for host-microbiome co-evolution in apple
- 2022
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 234:6, s. 2088-2100
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Tidskriftsartikel (refereegranskat)abstract
- Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host–microbiome co-evolutionary dynamics are poorly understood.Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species.The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome.This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.
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| 3. |
- Abdelfattah, Ahmed, et al.
(författare)
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Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root
- 2021
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 23:4, s. 2199-2214
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Tidskriftsartikel (refereegranskat)abstract
- While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities.
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| 4. |
- Abdelfattah, Ahmed, et al.
(författare)
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From seed to seed : the role of microbial inheritance in the assembly of the plant microbiome
- 2023
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Ingår i: Trends in Microbiology. - : Elsevier BV. - 0966-842X .- 1878-4380. ; 31:4, s. 346-355
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Forskningsöversikt (refereegranskat)abstract
- Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host–microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.
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| 5. |
- Abrego, Nerea, et al.
(författare)
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Accounting for environmental variation in co-occurrence modelling reveals the importance of positive interactions in root-associated fungal communities
- 2020
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 29:14, s. 2736-2746
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing the role of interspecific interactions in determining community structure is to identify the species co-occurrences that are not constrained by environmental conditions. In this study, we investigated co-occurrences among root-associated fungi, asking whether fungi co-occur more or less strongly than expected based on the environmental conditions and the host plant species examined. We generated molecular data on root-associated fungi of five plant species evenly sampled along an elevational gradient at a high arctic site. We analysed the data using a joint species distribution modelling approach that allowed us to identify those co-occurrences that could be explained by the environmental conditions and the host plant species, as well as those co-occurrences that remained unexplained and thus more probably reflect interactive associations. Our results indicate that not only negative but also positive interactions play an important role in shaping microbial communities in arctic plant roots. In particular, we found that mycorrhizal fungi are especially prone to positively co-occur with other fungal species. Our results bring new understanding to the structure of arctic interaction networks by suggesting that interactions among root-associated fungi are predominantly positive.
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| 6. |
- Abrego, Nerea, et al.
(författare)
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Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient
- 2020
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 10:16, s. 8989-9002
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Tidskriftsartikel (refereegranskat)abstract
- How community-level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root-associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root-associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root-associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root-associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root-associated fungal communities.
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| 7. |
- Ayalew Nurihun, Biruk, 1983-
(författare)
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The relationship between climate, disease and coffee yield: optimizing management for smallholder farmers
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Climate change and diseases are threatening global crop production. Agroforestry systems, which are characterized by complex multispecies interactions, are considered to provide nature-based solutions for climate change mitigation and pest and disease regulation. Understanding the role of the abiotic environment and species interactions in shaping diseases and yield in agroforestry systems would enable us to develop effective ecologically-informed pest and disease management under a changing climate, support sustainable agricultural practices, and maximize the benefits gained from agroforestry systems. To gain such a comprehensive understanding of what shapes pest and disease levels and yield in agroforestry systems, we need to investigate how the interactions between agroforestry system components, such as trees, crops and their associated organisms, vary in space and time, and how they are influenced by abiotic factors in terms of pests and diseases and yield. In this thesis, my overarching goal was to understand how microclimate and management impact major coffee pests and diseases, their natural enemies, and coffee yield, as well as farmers’ perceptions of climate change and climate-mediated changes in disease dynamics and yield, with the aim of using these insights to optimize management decisions for smallholder farmers in southwestern Ethiopia. With this aim, I selected 58 sites along a gradient of management intensity, ranging from minimal management in the natural forest to moderate management in smallholder farms and intensive management in commercial plantations. As an approach, I combined observational and interview studies to examine i) the impact of shade tree species identity and canopy cover on coffee pests and diseases, ii) the effect of climate and management on coffee berry disease and yield, iii) the impact of climate on a host-hyperparasite interaction, and iv) farmers’ perceptions of climate change and climate-mediated changes in disease dynamics and yield. I found that tree identity affected the incidence and severity of coffee diseases, whereas insect pests were strongly affected by canopy cover, but in a species-specific way (I). Both climate and management affected coffee berry disease and yield. Importantly, the effect of climatic variables on disease and yield differed strongly between the developmental stages from flowering to ripening (II). In chapter (III), I found that the climatic niches of coffee leaf rust and its hyperparasite differed, with coffee leaf rust severity preferring high maximum temperatures, whereas the hyperparasite preferred cold nights. The interviews revealed that the majority of farmers perceived long-term changes in one or more aspects of the climate, and the majority of farmers perceived an increase in coffee leaf rust and a decrease in coffee berry disease. Climate data also supported farmers’ knowledge on climate-disease-yield relationships (IV). Taken together, my thesis advances our understanding of the relationship between climate and management of coffee pests, diseases and yield, and this may contribute to the development of ecologically-informed pest and disease management strategies for coffee production and other agroforestry crops.
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| 8. |
- Barr, Anna E., et al.
(författare)
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Local habitat factors and spatial connectivity jointly shape an urban insect community
- 2021
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Ingår i: Landscape and Urban Planning. - : Elsevier BV. - 0169-2046 .- 1872-6062. ; 214
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Tidskriftsartikel (refereegranskat)abstract
- As the world becomes more and more urbanized, it is increasingly important to understand the impacts of urban landscapes on biodiversity. Urbanization can change local habitat factors and decrease connectivity among local habitats, with major impacts on the structure of natural food webs. However, most studies have focused on single species, or compared rural to urban habitats, which do not inform us on how to design and manage cities to optimize biodiversity. To understand the local and spatial drivers of ecological communities within urban landscapes, we assessed the relative impact of local habitat factors (sunlight exposure and leaf litter) and spatial connectivity on an oak-associated herbivore community within an urban landscape. From the local habitat factors, leaf litter but not sunlight exposure was related to herbivore species richness, with leaf litter contributing to the maintenance of high species richness on isolated trees. Guilds and species differed strongly in their response to local habitat factors and connectivity, resulting in predictable variation in insect community composition among urban oaks. Taken together, our study shows an interactive effect of local and spatial factors on species richness and species composition within an urban context, with guild- and species-specific life histories determining the response of insects to urban landscapes. To maintain biodiversity in the urban landscape, preserving a dense network of local habitats is essential. Moreover, allowing leaf litter to accumulate can be a simple, cost-effective conservation management practice.
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| 9. |
- Beche, Dinkissa, et al.
(författare)
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Prevalence of major pests and diseases in wild and cultivated coffee in Ethiopia
- 2023
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Ingår i: Basic and Applied Ecology. - 1439-1791 .- 1618-0089. ; 73, s. 3-9
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Tidskriftsartikel (refereegranskat)abstract
- The study of pests and diseases on crops and crop relatives in the wild is valuable from both a theoretical and an applied point of view. Few studies have addressed multiple pests and diseases in such ecosystems. Our objectives were to (1) compare the prevalence of multiple pests and diseases on coffee in forests and more managed landscapes and (2) assess how spatial, environmental, host density and management factors affect the incidence and severity of coffee pests and diseases across forests.To achieve these objectives we studied different pests, diseases and one hyperparasite on wild and semi-wild coffee from 84 plots of 20 × 20 m across a forested landscape in southwest Ethiopia and compared the results to previous studies of more intensively managed adjacent landscapes.The prevalence of all surveyed coffee leaf pests and diseases was high (>71% of investigated plots) and very similar to the levels in more intensively managed landscapes reported in the literature. The incidence rates of all pests, diseases and the hyperparasite showed a high variation among the plots, and correlation with each other in some cases. However, this variation was weakly related to the measured environmental and management variables, but coffee pests and diseases were often positively related to high coffee density.One possible explanation for the similar prevalence is that, although the landscapes are different, the local environmental conditions have much in common since coffee is also grown under indigenous shade trees in more intensively managed landscapes. However, the variability in pest and disease levels among sites was large and it is difficult to predict where they attain high levels. There is a need of detailed investigations on drivers of spatio-temporal population dynamics of these species, including their natural enemies, to be able to provide advice for development of sustainable coffee disease management.
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| 10. |
- Beche, Dinkissa, et al.
(författare)
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Spatial variation in human disturbances and their effects on forest structure and biodiversity across an Afromontane forest
- 2022
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Ingår i: Landscape Ecology. - : Springer Science and Business Media LLC. - 0921-2973 .- 1572-9761. ; 37:2, s. 493-510
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Tidskriftsartikel (refereegranskat)abstract
- Context Human disturbances can have large impacts on forest structure and biodiversity, and thereby result in forest degradation, a property difficult to detect by remote sensing.Objectives To investigate spatial variation in anthropogenic disturbances and their effects on forest structure and biodiversity.Methods In 144 plots of 20 x 20 m distributed across a forest area of 750 km2 in Southwest Ethiopia, we recorded: landscape variables (e.g., distance to forest edge), different human disturbances, forest structure variables, and species composition of trees and epiphyllous bryophytes. We then first assessed if landscape variables could explain the spatial distribution of disturbances. Second, we analysed how forest structure and biodiversity were influenced by disturbances.Results Human disturbances, such as coffee management and grazing declined with distance to forest edges, and penetrated at least a kilometer into the forest. Slope was not related to disturbance levels, but several types of disturbances were less common at higher elevations. Among human disturbance types, coffee management reduced liana cover and was associated with altered species composition of trees. The presence of large trees and basal area were not related to any of the disturbance gradients.Conclusions Although most anthropogenic disturbances displayed clear edge effects, surprisingly the variation in the chosen forest degradation indices were only weakly related to these disturbances. We suggest that the intersection between edge effects and forest degradation is very context specific and relies much on how particular societies use the forests. For example, in this landscape coffee management seems to be a key driver.
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