| 1. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Mycobiome diversity: high-throughput sequencing and identification of fungi.
- 2019
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Ingår i: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109
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Forskningsöversikt (refereegranskat)abstract
- Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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| 2. |
- Baresel, Christian, et al.
(författare)
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Uncertainty-Accounting Environmental Policy and Management of Water Systems
- 2007
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Ingår i: Environmental Science & Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 41:10, s. 3653–3659-
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Tidskriftsartikel (refereegranskat)abstract
- Environmental policies for water quality and ecosystemmanagement do not commonly require explicit stochasticaccounts of uncertainty and risk associated with thequantification and prediction of waterborne pollutant loadsand abatement effects. In this study, we formulate andinvestigate a possible environmental policy that does requirean explicit stochastic uncertainty account. We compareboth the environmental and economic resource allocationperformance of such an uncertainty-accounting environmentalpolicy with that of deterministic, risk-prone and riskaverseenvironmental policies under a range of differenthypothetical, yet still possible, scenarios. The comparisonindicates that a stochastic uncertainty-accountingpolicy may perform better than deterministic policies overa range of different scenarios. Even in the absence ofreliable site-specific data, reported literature values appearto be useful for such a stochastic account of uncertainty.
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| 3. |
- Sanli, Kemal, et al.
(författare)
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Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities
- 2015
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 6:1192
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Tidskriftsartikel (refereegranskat)abstract
- Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.
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| 4. |
- Cheung, Henry Lok Shan, et al.
(författare)
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Denitrification, anammox, and DNRA in oligotrophic continental shelf sediments
- 2024
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Ingår i: Limnology and Oceanography. - 1939-5590 .- 0024-3590.
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Tidskriftsartikel (refereegranskat)abstract
- Continental shelf sediments are considered hotspots for nitrogen (N) removal. While most investigations have quantified denitrification in shelves receiving large amounts of anthropogenic nutrient supply, we lack insight into the key drivers of N removal on oligotrophic shelves. Here, we measured rates of N removal through denitrification and anammox by the revised-isotope pairing technique (r-IPT) along the Northeastern New Zealand shelf. Denitrification dominated total N2 production at depths between 30 and 128 m with average rates (± SE) ranging from 65 ± 28 to 284 ± 72 μmol N m−2 d−1. N2 production by anammox ranged from 3 ± 1 to 28 ± 11 μmol N m−2 d−1 and accounted for 2–19% of total N2 production. DNRA was negligible in these oligotrophic settings. Parallel microbial community analysis showed that both Proteobacteria and Planctomycetota were key taxa driving denitrification. Denitrification displayed a negative correlation with oxygen penetration depth, and a positive correlation with macrofauna abundance. Our denitrification rates were comparable to oligotrophic shelves from the Arctic, but were lower than those from nutrient-rich Pacific and Atlantic shelves. Based on our results and existing IPT measurements, the global shelf denitrification rate was reassessed to be 53.5 ± 8.1 Tg N yr−1, equivalent to 20 ± 2% of marine N removal. We suggest that previous estimates of global shelf N loss might have been overestimated due to sampling bias toward areas with high N loads in the Northern Hemisphere.
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| 5. |
- Sonesten, Lars
(författare)
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Miljöövervakningen av Sveriges sjöar och vattendrag : Representativiteten av den kontrollerande miljöövervakningen
- 2013
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Samtliga ytvattenkategorier inom ett vattendistrikt ska omfattas av övervakningsprogram inklusive övervakningsnät för kontrollerande övervakning som upprättas enligt kap. 7 VFF. En översyn av hur representativt Sveriges kontrollerade övervakningsnät är har tidigare inte kunnat utföras på grund av omfattande kvalitetsbrister i länsstyrelserna och vattenmyndigheternas datasystem VISS (VattenInformationsSystem Sverige). Kvaliteten på informationen i VISS har under senare år genomgått en omfattande kvalitetssäkring, vilket har gett förutsättningarna för att nu kunna genomföra den sammanställning och översyn över den svenska miljöövervakningen av sjöar och vattendrag. Denna översyn har varit starkt önskad under flera år, då det finns ett stort behov av att se över och analysera hur ett representativt samordnat kontrollerande övervakningsprogram skulle kunna se ut. Översynen sker mot bakgrund av den samlade vatten övervakning som bedrivs i Sverige, bland annat för att optimera befintlig övervakning och att kunna förstärka den där brister har identifierats. Arbetet är också viktigt för att säkerställa att kommande rapporteringar såväl internationellt som nationellt blir så bra som möjligt.Uppdraget för projektet Representativ kontrollerande miljöövervakning (RepKöp) syftar till att ta fram ett förslag på hur ett representativt kontrollerande övervakningsprogram med avseende på (vattentyper), kvalitetsfaktorer och statusklasser bör se ut på nationell och distriktsnivå i Sverige. Förslaget tas fram mot bakgrund av den samlade vattenövervakningen som bedrivs i Sverige idag och mot bakgrund av vad behövs för att uppfylla vattendirektivets krav på kontrollerande övervakning av vattenförekomster.Resultaten från översynen är tänkta att dels fungera som underlag för att underlätta Havs och vattenmyndighetens och Vattenmyndigheternas arbete inför rapporteringen 2012, men framför allt ska projektet ge underlag för att ta fram optimerade övervakningsprogram för sjöar och vattendrag till en långsiktig plan med en första anhalt 2016. För att RepKÖP ska få praktisk betydelse i övervakningsSverige skall projektet resultera i ett underlag för framtida revision av befintliga övervakningsprogram för respektive distrikt.Arbetet inom RepKöp är uppdelat i flera delar, vilka tillsammans ska fungera som vägledning till:• Vattenförvaltningens arbete med kontrollerande övervakning• Upplägg av nationell och regional miljöövervakningMålgruppen för arbetet är i första hand:• Vattenmyndigheter• Länsstyrelserna• Naturvårdsverket• Havs och vattenmyndigheten• Datavärdar och utförare av miljöövervakningFöreliggande rapport är en sammanställning och analys av miljöövervakningen av svenska sjöar och vattendrag så som de beskrevs i VISS vid datauttaget för sjöar i oktober 2011 och vattendrag i maj 2012. Sammanställningen av informationen från VISS har initierat en hel del korrigeringar i systemet, men tyvärr har det inte av praktiska skäl varit möjligt att ta hänsyn till dessa i arbetet. Man skall vara medveten om att VISS är en levande databas som ständigt uppdateras och korrigeras, vilket gör att endast en ”ögonblicksbild” kan analyseras. Detta gör att när analysen är färdig har verkligheten med stor sannolikhet redan till viss del hunnit förändrats.
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| 6. |
- Wurzbacher, Christian, 1980, et al.
(författare)
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Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.
- 2017
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Ingår i: The ISME journal. - : Springer Science and Business Media LLC. - 1751-7370 .- 1751-7362. ; 11:8, s. 1938-1941
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Tidskriftsartikel (refereegranskat)abstract
- In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.
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| 7. |
- Roth, Florian, et al.
(författare)
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High spatiotemporal variability of methane concentrations challenges estimates of emissions across vegetated coastal ecosystems.
- 2022
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Ingår i: Global change biology. - : Wiley. - 1365-2486 .- 1354-1013. ; 28:14, s. 4308-4322
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Tidskriftsartikel (refereegranskat)abstract
- Coastal methane (CH4 ) emissions dominate the global ocean CH4 budget and can offset the "blue carbon" storage capacity of vegetated coastal ecosystems. However, current estimates lack systematic, high-resolution, and long-term data from these intrinsically heterogeneous environments, making coastal budgets sensitive to statistical assumptions and uncertainties. Using continuous CH4 concentrations, δ13 C-CH4 values, and CH4 sea-air fluxes across four seasons in three globally pervasive coastal habitats, we show that the CH4 distribution is spatially patchy over meter-scales and highly variable in time. Areas with mixed vegetation, macroalgae, and their surrounding sediments exhibited a spatiotemporal variability of surface water CH4 concentrations ranging two orders of magnitude (i.e., 6-460nM CH4 ) with habitat-specific seasonal and diurnal patterns. We observed (1) δ13 C-CH4 signatures that revealed habitat-specific CH4 production and consumption pathways, (2) daily peak concentration events that could change >100% within hours across all habitats, and (3) a high thermal sensitivity of the CH4 distribution signified by apparent activation energies of ~1eV that drove seasonal changes. Bootstrapping simulations show that scaling the CH4 distribution from few samples involves large errors, and that ~50 concentration samples per day are needed to resolve the scale and drivers of the natural variability and improve the certainty of flux calculations by up to 70%. Finally, we identify northern temperate coastal habitats with mixed vegetation and macroalgae as understudied but seasonally relevant atmospheric CH4 sources (i.e., releasing≥100μmol CH4 m-2 day-1 in summer). Due to the large spatial and temporal heterogeneity of coastal environments, high-resolution measurements will improve the reliability of CH4 estimates and confine the habitat-specific contribution to regional and global CH4 budgets.
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| 8. |
- Khatami, Sina, et al.
(författare)
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What is drought? The scientific understanding of drought: the primary step towards resolving Iran's water crisis
- 2015
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Ingår i: Etemad Daily Newspaper, No. 3193. ; , s. 7-7
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- Abstract in Uncoded languagesIn this article we discuss four basic approaches to characterising droughts namely meteorological, hydrological, agricultural, and socioeconomic. In the first three approaches, drought is defined and measured as a physical phenomenon primarily related to the precipitation shortfall. Socioeconomic drought, nonetheless, is described and determined as the 'supply' and 'demand' in terms of water shortage in different socioeconomic systems. The specific case of Iran’s drought and water crisis is the main focus of this article, and is briefly compared to California’s ongoing drought. In cases such as Iran, the socioeconomic drought is a result of inefficient and unsustainable management of water resources. Therefore, we cannot simply associate droughts with climate variability and/or change. Furthermore, due to large uncertainties in climate modelling and water management scenarios, long-term prediction of drought is impossible.
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| 9. |
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| 10. |
- Gerlee, Philip, 1980, et al.
(författare)
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Scientific Models : Red Atoms, White Lies and Black Boxes in a Yellow Book
- 2016
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches and techniques. It provides a comprehensive introduction to scientific models and shows how models are constructed and used in modern science. It also addresses the approach to, and the culture surrounding modelling in different scientific disciplines. It serves as an inspiration for model building and also facilitates interdisciplinary collaborations by showing how models are used in different scientific fields. The book is aimed primarily at students in the sciences and engineering, as well as students at teacher training colleges but will also appeal to interested readers wanting to get an overview of scientific modelling in general and different modelling approaches in particular.
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