Effects of long-term N fertilization on nitrate leaching and vegetation responses in a spruce stand after severe wind damage

Wind damage in a forest stand can result in varying soil effects depending on the pre-history of the site, but areas with storm-felled trees can generally be expected to show more nitrate leaching than undamaged stands. Previous fertilization in such areas, especially with nitrogen (N) fertilizer, may further increase nitrate leaching. This study examined the effect of partial felling of a 42-year-old Norway spruce stand in the Skogaby experimental forest in Sweden during Storm Gudrun in 2005. Nitrate leaching was measured one year before and six years after the storm, in three experimental treatments: fertilization-irrigation with complete nutrient admixture (IF), fertilization with N-free nutrient admixture (V), and an untreated control (0). The 0 and IF treatments had some undamaged replicate plots, but V plots had no trees left after the storm. Compared with undamaged plots and the pre-disturbance level, nitrate leaching was significantly higher in all storm-felled plots, and in the soil solution nitrate dominated strongly over ammonium. Leaching peaked during the second and third post-storm years (2006-2007) and decreased to near pre-storm levels during the fifth and sixth years (2009-2010). Total nitrate leaching 2005-2010 was estimated to be 414, 233, and 218 kg N ha(-1) in the damaged IF, 0, and V plots, respectively. Total nitrate leaching in undisturbed plots in the IF and 0 treatments was 37 and 0.3 kg N ha(-1), respectively. Ground vegetation coverage, biomass, and biomass N increased with time and were negatively correlated with nitrate discharge. However, plant uptake of N only partly explained the significant decline in nitrate leaching between 2006 and 2010. This decrease could also be explained by N immobilization in fungi decomposing woody roots with low N concentrations

SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing

From Springer Nature via Jisc Publications RouterHistory: received 2022-04-21, rev-recd 2022-09-08, accepted 2022-10-05, registration 2022-10-10, pub-electronic 2022-10-18, online 2022-10-18, collection 2022-12Acknowledgements: Acknowledgements: We are immensely grateful to all our co-workers at the Section for Clinical Microbiology and Hospital Hygiene at Uppsala University Hospital, who PCR tested all the COVID-19 samples and consequently extracted the viral RNA for us from the positive samples. Secondly, we are deeply thankful to Tor-Elesh Albrigtsen for the remarkable assistance with data science, analysis and programming in Python.Publication status: PublishedFunder: Science for Life Laboratory; doi: http://dx.doi.org/10.13039/501100009252; Grant(s): ZSC – National core facility for pandemic preparednessFunder: Scandinavian Society for Antimicrobial Chemotherapy Foundation; doi: http://dx.doi.org/10.13039/501100011777; Grant(s): SLS-961049Funder: Erik, Karin and Gösta Selander Foundation; Grant(s): 2022Funder: Regionala Forskningsrådet Uppsala/Örebro; doi: http://dx.doi.org/10.13039/100019032; Grant(s): RFR-930984Funder: Uppsala UniversityAbstract: Background: Since the beginning of the COVID-19 pandemic, new variants of significance to public health have emerged. Consequently, early detection of new mutations and variants through whole-genome sequencing remains crucial to assist health officials in employing appropriate public health measures. Methods: We utilized the ARTIC Network SARS-CoV-2 tiled amplicon approach and Nanopore sequencing to sequence 4,674 COVID-19 positive patient samples from Uppsala County, Sweden, between week 15 and 52 in 2021. Using this data, we mapped the circulating variants of concern (VOC) in the county over time and analysed the Spike (S) protein mutational dynamics in the Delta variant throughout 2021. Results: The distribution of the SARS-CoV-2 VOC matched the national VOC distribution in Sweden, in 2021. In the S protein of the Delta variant, we detected mutations attributable to variants under monitoring and variants of interest (e.g., E484Q, Q613H, Q677H, A222V and Y145H) and future VOC (e.g., T95I and Y144 deletion, which are signature mutations in the Omicron variant). We also frequently detected some less well-described S protein mutations in our Delta sequences, that might play a role in shaping future emerging variants. These include A262S, Q675K, I850L, Q1201H, V1228L and M1237I. Lastly, we observed that some of the Delta variant’s signature mutations were underrepresented in our study due to artifacts of the used bioinformatics tools, approach and sequencing method. We therefore discuss some pitfalls and considerations when sequencing SARS-CoV-2 genomes. Conclusion: Our results suggest that genomic surveillance in a small, representative cohort can be used to make predictions about the circulating variants nationally. Moreover, we show that detection of transient mutations in currently circulating variants can give valuable clues to signature mutations of future VOC. Here we suggest six such mutations, that we detected frequently in the Delta variant during 2021. Lastly, we report multiple systematic errors that occurred when following the ARTIC Network SARS-CoV-2 tiled amplicon approach using the V3 primers and Nanopore sequencing, which led to the masking of some of the important signature mutations in the Delta sequences

Long-term effects of enhanced nitrogen and sulphate additions on soil acidification and nutrient cycling in a Norway spruce stand

This thesis describes the long-term effects of enhanced inputs of ammonium and sulphate (NS) in a spruce stand in SW Sweden on the accumulation and fluxes of nutrients in above and below ground biomass, soil chemistry and leaching of nutrients. Ammonium and sulphate were added annually at a rate of 100 kg N and 114 kg kg S ha'1, which was five to six times higher than the deposition rate of the study area. The main nutrients studied were N, P, K, Ca, Mg and S. Other important parameters were pH, NH4, N 0 3 and A1 in soil, soil solution and deposition. The addition of NS decreased the pH in the mineral soil by 0.4 units and in the soil solution by 0.3 units. The increased acidity of the soil was almost totally buffered by dissolution of solid aluminium compounds (gibbsite). The input of inorganic nitrogen by deposition was totally retained in the ecosystem, as the stand was unsaturated with respect to nitrogen. The high additional input of nitrogen soon turned the stand into a nitrogensaturated system. About 40% of the Mg was leached from the humus layer. The NS treatment increased the leaching of all nutrients except P and K from the root zone and the water soluble concentrations of all nutrients except NH4 and S04 increased in the rhizosphere soil. The amount of fine roots (<2mm) decreased in the humus layer but increased in mineral soil and was unaffected overall when both humus and mineral soil were taken into consideration. The uptake of Ca and Mg by fine roots was blocked by ammonium in the forest floor and by ammonium and aluminium in the mineral soil. The concentrations of these nutrients decreased in the fine roots and also in the needles. The annual accumulation of N during the first six years (1988-1993) in the above and below ground biomass increased by a factor of 9 compared to control (C ) plots. However, the accumulation of P, K, Ca, Mg and S was less than double the C level. During the six year treatment, the above ground biomass increased by 47% relative to C plots. During the following years (until 1998) the yearly basal area increment in NS plots decreased and in 1997 it was lower than in C plots. Changes in the nutrient concentration in needles indicated that deficiency of P, K and later Mg could be the reason for the growth decline. It is suggested that high NS addition may increase biomass production in a short-term perspective, although not without negative effects on soil and soil solution. In a long-term perspective, it will lead to a strong disturbance both of the stand and its environment in the form of acidified soils and high leaching rate of nutrients and aluminium to groundwater

Transcriptomic isolation and sequencing of the freshwater mussel Anodonta anatina : A pilot study and method development

The freshwater mussel Anodonta anatina is a common mollusc found in rivers and lakes in Europe. Due to its lifestyle as an immobile substrate filter feeder, it is only exposed to pollutions which passes by it, thus the mussels are viable to be used as a bioindicator for the analysis of local aquatic health. With the recent decades of advancements in nucleotide sequencing platforms, transcriptomic analysis could be utilized to make an assessment of the quality of water, as the transcriptome of organisms respond to the presence of toxins and changes in the environment. The aim of this project was to develop a method to isolate and sequence the transcriptome of the hepatopancreas of the freshwater mussel A. anatina with an Oxford MinION nanopore sequencer. The method used two samples collected from a previous study where one mussel, named “unexposed sample 05H” for this thesis, was used as a control while the second sample, named “exposed sample 08H”, was exposed to 100 μg Cu2+/L. The method processed 80 mg of hepatopancreatic tissue and measured a 99.7 % drop in RNA during the five different protocols utilized. The method produced viable data, and the web based bioinformatic program NanoPipe managed to identify homologous sequences to the genome of the Mediterranean mussel Mytilus galloprovincialis. Due to a low number of samples, no comparative study of coppers effect on the transcriptome could be made

Positionering och Spårning av mobila enheter, ur ett IT–forensiskt perspektiv

I dagens Sverige så har de mobila enheterna en självklar plats i våra fickor, likväl som i vårt samhälle och i dess brottslighet, vilket gör att det sedan några år är att anse självklart att de även har en central roll i IT–forensiska utredningar inom våra polismyndigheter. Men vid sidan av konkreta bevis för begångna brott lagrar enheterna dessutom ofta data som kan användas för att spåra enheten, och därmed också dess brukare, över tid, vilket givetvis är av intresse av polismyndigheter men skulle även kunna vara av stort intresse för exempelvis försäkringsbolag och andra delar av den 'civila sektorn' som driver utredningar men som saknar polisens befogenheter. För att ge ett så brett användningsområde som möjligt fokuserar därför rapporten inte bara på datat som är tillgängligt från den faktiska enheten och hur de kan användas för spårning och positionering, utan försöker även på praktiskt väg undersöka i vilken grad dessa metoder kan utföras med allmänt tillgänglig mjuk- och hårdvara

Effects of long-term N fertilization on nitrate leaching and vegetation responses in a spruce stand after severe wind damage

Wind damage in a forest stand can result in varying soil effects depending on the pre-history of the site, but areas with storm-felled trees can generally be expected to show more nitrate leaching than undamaged stands. Previous fertilization in such areas, especially with nitrogen (N) fertilizer, may further increase nitrate leaching. This study examined the effect of partial felling of a 42-year-old Norway spruce stand in the Skogaby experimental forest in Sweden during Storm Gudrun in 2005. Nitrate leaching was measured one year before and six years after the storm, in three experimental treatments: fertilization-irrigation with complete nutrient admixture (IF), fertilization with N-free nutrient admixture (V), and an untreated control (0). The 0 and IF treatments had some undamaged replicate plots, but V plots had no trees left after the storm. Compared with undamaged plots and the pre-disturbance level, nitrate leaching was significantly higher in all storm-felled plots, and in the soil solution nitrate dominated strongly over ammonium. Leaching peaked during the second and third post-storm years (2006-2007) and decreased to near pre-storm levels during the fifth and sixth years (2009-2010). Total nitrate leaching 2005-2010 was estimated to be 414, 233, and 218 kg N ha(-1) in the damaged IF, 0, and V plots, respectively. Total nitrate leaching in undisturbed plots in the IF and 0 treatments was 37 and 0.3 kg N ha(-1), respectively. Ground vegetation coverage, biomass, and biomass N increased with time and were negatively correlated with nitrate discharge. However, plant uptake of N only partly explained the significant decline in nitrate leaching between 2006 and 2010. This decrease could also be explained by N immobilization in fungi decomposing woody roots with low N concentrations

SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing.

From PubMed via Jisc Publications RouterHistory: received 2022-04-21, revised 2022-09-08, accepted 2022-10-05Publication status: epublishFunder: Science for Life Laboratory; Grant(s): ZSC - National core facility for pandemic preparednessFunder: Scandinavian Society for Antimicrobial Chemotherapy Foundation; Grant(s): SLS-961049Funder: Erik, Karin and Gösta Selander Foundation; Grant(s): 2022Funder: Regionala Forskningsrådet Uppsala/Örebro; Grant(s): RFR-930984Since the beginning of the COVID-19 pandemic, new variants of significance to public health have emerged. Consequently, early detection of new mutations and variants through whole-genome sequencing remains crucial to assist health officials in employing appropriate public health measures. We utilized the ARTIC Network SARS-CoV-2 tiled amplicon approach and Nanopore sequencing to sequence 4,674 COVID-19 positive patient samples from Uppsala County, Sweden, between week 15 and 52 in 2021. Using this data, we mapped the circulating variants of concern (VOC) in the county over time and analysed the Spike (S) protein mutational dynamics in the Delta variant throughout 2021. The distribution of the SARS-CoV-2 VOC matched the national VOC distribution in Sweden, in 2021. In the S protein of the Delta variant, we detected mutations attributable to variants under monitoring and variants of interest (e.g., E484Q, Q613H, Q677H, A222V and Y145H) and future VOC (e.g., T95I and Y144 deletion, which are signature mutations in the Omicron variant). We also frequently detected some less well-described S protein mutations in our Delta sequences, that might play a role in shaping future emerging variants. These include A262S, Q675K, I850L, Q1201H, V1228L and M1237I. Lastly, we observed that some of the Delta variant's signature mutations were underrepresented in our study due to artifacts of the used bioinformatics tools, approach and sequencing method. We therefore discuss some pitfalls and considerations when sequencing SARS-CoV-2 genomes. Our results suggest that genomic surveillance in a small, representative cohort can be used to make predictions about the circulating variants nationally. Moreover, we show that detection of transient mutations in currently circulating variants can give valuable clues to signature mutations of future VOC. Here we suggest six such mutations, that we detected frequently in the Delta variant during 2021. Lastly, we report multiple systematic errors that occurred when following the ARTIC Network SARS-CoV-2 tiled amplicon approach using the V3 primers and Nanopore sequencing, which led to the masking of some of the important signature mutations in the Delta sequences. [Abstract copyright: © 2022. The Author(s).

Mineralogy and biogeochemistry of potassium in the Skogaby experimental forest, southwest Sweden: pools, fluxes and K/Rb ratios in soil and biomass

Clay minerals and K feldspars were evaluated as sources of K in a Norway spruce stand (Picea abies (L.) Karst.) from the Skogaby experimental forest in southwest Sweden. The soil, developed in a Quaternary glacial till, has only 3-5% clay, and more than 95% of its K resides in feldspars. Ratios of K/Rb were assessed in interlayers of 2: 1 clay minerals (extracted with hot (100 degrees C) 2 M HCl), biomass and the forest floor. These compartments had similarly low K/Rb ratios, whereas K feldspars were significantly poorer in Rb. A fractionation model indicated preferential retention of Rb in the biomass and forest floor, due to stronger adsorption of Rb than K in the humus, as well as preferential uptake of K from the exchange complex in the mineral soil. Preferential uptake of K may result from weaker adsorption of K by the cation exchanger, or preference for dissolved K over Rb by the roots. A quantitative mineralogical analysis revealed that loss from micas may account for half of the Holocene loss of K from the soil, which was approximately 22 Mg ha(-1). Exceptionally low K/Rb ratios in HCl extracts of the upper 60 cm of the profile indicated extensive loss of K from mica in the parent material and re-fixation of K and Rb at lower ratios. The results indicate that fixation in and release from clay minerals may be prominent in the cycling of K, even in a soil that is poor in clay minerals

In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation

We describe a flight-associated infection scenario of seven individuals with a B.1.617.2 (Delta) lineage, harbouring an S:E484Q point mutation. In Sweden, at least 10% of all positive SARS-CoV-2 samples were sequenced in each county; the B.1.717.2 + S:E484Q combination was not detected in Sweden before and was imported within the scenario described in this report. The high transmission rate of the delta lineage combined with the S:E484Q mutation, associated with immune escape in other lineages, makes this specific genetic combination a possible threat to the global fight against the COVID-19 pandemic. Even within the Omicron wave, the B.1.617.2 + S:E484Q variant appeared in community samples in Sweden, as it seems that this combination has an evolutionary gain compared to other B.1.617.2 lineages. The here described genomic combination was not detectable with the common fasta file-based Pango-lineage analysis, hence increasing the probability of the true global prevalence to be higher