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- Weldatsadik, RG, et al.
(författare)
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Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus
- 2017
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7, s. 45771-
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of the genomic variation among different strains of a pathogenic microbial species can help in selecting optimal candidates for diagnostic assays and vaccine development. Pooled sequencing (Pool-seq) is a cost effective approach for population level genetic studies that require large numbers of samples such as various strains of a microbe. To test the use of Pool-seq in identifying variation, we pooled DNA of 100 Streptococcus pyogenes strains of different emm types in two pools, each containing 50 strains. We used four variant calling tools (Freebayes, UnifiedGenotyper, SNVer, and SAMtools) and one emm1 strain, SF370, as a reference genome. In total 63719 SNPs and 164 INDELs were identified in the two pools concordantly by at least two of the tools. Majority of the variants (93.4%) from six individually sequenced strains used in the pools could be identified from the two pools and 72.3% and 97.4% of the variants in the pools could be mined from the analysis of the 44 complete Str. pyogenes genomes and 3407 sequence runs deposited in the European Nucleotide Archive respectively. We conclude that DNA sequencing of pooled samples of large numbers of bacterial strains is a robust, rapid and cost-efficient way to discover sequence variation.
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- Chrysafi, Anna, et al.
(författare)
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Quantifying Earth system interactions for sustainable food production via expert elicitation
- 2022
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Ingår i: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 5:10, s. 830-842
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Tidskriftsartikel (refereegranskat)abstract
- Several safe boundaries of critical Earth system processes have already been crossed due to human perturbations; not accounting for their interactions may further narrow the safe operating space for humanity. Using expert knowledge elicitation, we explored interactions among seven variables representing Earth system processes relevant to food production, identifying many interactions little explored in Earth system literature. We found that green water and land system change affect other Earth system processes strongly, while land, freshwater and ocean components of biosphere integrity are the most impacted by other Earth system processes, most notably blue water and biogeochemical flows. We also mapped a complex network of mechanisms mediating these interactions and created a future research prioritization scheme based on interaction strengths and existing knowledge gaps. Our study improves the understanding of Earth system interactions, with sustainability implications including improved Earth system modelling and more explicit biophysical limits for future food production.
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- Keuper, Frida, et al.
(författare)
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Carbon loss from northern circumpolar permafrost soils amplified by rhizosphere priming
- 2020
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Ingår i: Nature Geoscience. - : Springer Science and Business Media LLC. - 1752-0894 .- 1752-0908. ; 13, s. 560-565
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Tidskriftsartikel (refereegranskat)abstract
- As global temperatures continue to rise, a key uncertainty of climate projections is the microbial decomposition of vast organic carbon stocks in thawing permafrost soils. Decomposition rates can accelerate up to fourfold in the presence of plant roots, and this mechanism-termed the rhizosphere priming effect-may be especially relevant to thawing permafrost soils as rising temperatures also stimulate plant productivity in the Arctic. However, priming is currently not explicitly included in any model projections of future carbon losses from the permafrost area. Here, we combine high-resolution spatial and depth-resolved datasets of key plant and permafrost properties with empirical relationships of priming effects from living plants on microbial respiration. We show that rhizosphere priming amplifies overall soil respiration in permafrost-affected ecosystems by similar to 12%, which translates to a priming-induced absolute loss of similar to 40 Pg soil carbon from the northern permafrost area by 2100. Our findings highlight the need to include fine-scale ecological interactions in order to accurately predict large-scale greenhouse gas emissions, and suggest even tighter restrictions on the estimated 200 Pg anthropogenic carbon emission budget to keep global warming below 1.5 degrees C.
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