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1.
  • Nilsson, R. Henrik, 1976, et al. (författare)
  • Mycobiome diversity: high-throughput sequencing and identification of fungi.
  • 2019
  • Ingår i: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109
  • 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.
  • Sanli, Kemal, et al. (författare)
  • Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities
  • 2015
  • Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 6:1192
  • 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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3.
  • Kõljalg, Urmas, et al. (författare)
  • A price tag on species
  • 2022
  • Ingår i: Research Ideas and Outcomes_RIO. - : Pensoft Publishers. - 2367-7163. ; 8, s. 1-7
  • Tidskriftsartikel (refereegranskat)abstract
    • Species have intrinsic value but also partake in a long range of ecosystem services of major economic value to humans. These values have proved hard to quantify precisely, making it all too easy to dismiss them altogether. We outline the concept of the species stock market (SSM), a system to provide a unified basis for valuation of all living species. The SSM amalgamates digitized information from natural history collections, occurrence data, and molecular sequence databases to quantify our knowledge of each species from scientific, societal, and economic points of view. The conceptual trading system will necessarily be very unlike that of the regular stock market, but the looming biodiversity crisis implores us to finally put an open and transparent price tag on symbiosis, deforestation, and pollution
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4.
  • Nilsson, R. Henrik, 1976, et al. (författare)
  • Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms
  • 2022
  • Ingår i: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 239-244
  • Tidskriftsartikel (refereegranskat)abstract
    • DNA sequencing efforts of environmental and other biological samples disclose unprecedented and largely untapped opportunities for advances in the taxonomy, ecology, and geographical distributions of our living world. To realise this potential, DNA-derived occurrence data (notably sequences with dates and coordinates) – much like traditional specimens and observations – need to be discoverable and interpretable through biodiversity data platforms. The Global Biodiversity Information Facility (GBIF) recently headed a community effort to assemble a set of guidelines for publishing DNA-derived data. These guidelines target the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. They cover a choice of terms using a controlled vocabulary, common pitfalls, and good practices, without going into platform-specific details. Our hope is that they will benefit anyone interested in better exposure of DNA-derived occurrence data through general biodiversity data platforms, including national biodiversity portals. This paper provides a brief rationale and an overview of the guidelines, an up-to-date version of which is maintained at https://doi.org/10.35035/doc-vf1a-nr22. User feedback and interaction are encouraged as new techniques and best practices emerge.
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5.
  • Bengtsson-Palme, Johan, 1985, et al. (författare)
  • Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
  • 2013
  • Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 4:10, s. 914-919
  • Tidskriftsartikel (refereegranskat)abstract
    • The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.
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6.
  • Cafaro, Philip, et al. (författare)
  • Fewer people would help preserve biodiversity: A response to Hughes et al. (2023)
  • 2023
  • Ingår i: Biological Conservation. - 0006-3207. ; 282
  • Tidskriftsartikel (refereegranskat)abstract
    • “Smaller human populations are neither a necessary nor sufficient condition for biodiversity conservation,” according to Alice Hughes and colleagues. We agree that reducing human numbers is not sufficient for preserving biodiversity; whether it’s necessary depends on how high we set the bar for successful conservation. If we hope to preserve robust populations of most of the world’s remaining wild species and their habitats, the evidence suggests human populations will have to be considerably reduced.
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7.
  • Munthe, Christian, 1962 (författare)
  • Precaution and Ethics: Handling risks, uncertainties and knowledge gaps in the regulation of new biotechnologies
  • 2017
  • Bok (övrigt vetenskapligt/konstnärligt)abstract
    • This volume outlines and analyses ethical issues actualized by applying a precautionary approach to the regulation of new biotechnologies. It presents a novel way of categorizing and comparing biotechnologies from a precautionary standpoint. Based on this, it addresses underlying philosophical problems regarding the ethical assessment of decision-making under uncertainty and ignorance, and discusses how risks and possible benefits of such technologies should be balanced from an ethical standpoint. It argues on conceptual and ethical grounds for a technology neutral regulation as well as for a regulation that not only checks new technologies but also requires old, inferior ones to be phased out. It demonstrates how difficult ethical issues regarding the extent and ambition of precautionary policies need to be handled by such a regulation, and presents an overarching framework for doing so.
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8.
  • Hartmann, Martin, et al. (författare)
  • Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests
  • 2012
  • Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 6:12, s. 2199-2218
  • Tidskriftsartikel (refereegranskat)abstract
    • Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting.
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9.
  • Jayasiri, Subashini C., et al. (författare)
  • The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
  • 2015
  • Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18
  • Tidskriftsartikel (refereegranskat)abstract
    • Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
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10.
  • Unterseher, Martin, et al. (författare)
  • Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition
  • 2018
  • Ingår i: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 17:4, s. 489-500
  • Tidskriftsartikel (refereegranskat)abstract
    • Multiple biotic and abiotic parameters influence the dynamics of individual fungal species and entire communities. Major drivers for tropical plant endophytes are undoubtedly seasonality, local habitat conditions and biogeography. However, host specialization and tissue preferences also contribute to the structuring of endophytic mycobiomes. To elucidate such specializations and preferences, we sampled two commercially important, unrelated plant species, Amorphophallus albispathus and Camellia sinensis (tea plant) simultaneously at close proximity. The mycobiomes of different tissue types were assessed with high-throughput amplicon sequencing of the internal transcribed spacer DNA region. Both plants hosted different fungal communities and varied in α- and β-diversity, despite their neighboring occurrence. However, the fungal assemblages of Amorphophallus leaflets shared taxa with the mycobiomes of tea leaves, thereby suggesting common driving forces for leaf-inhabiting fungi irrespective of host plant identity. The mycobiome composition and diversity of tea leaves was clearly driven by leaf age. We suggest that the very youngest tea leaves are colonized by stochastic processes, while mycobiomes of old leaves are rather similar as the result of progressive succession. The biodiversity of fungi associated with A. albispathus was characterized by a large number of unclassified OTUs (at genus and species level) and by tissue-specific composition.This study is the first cultivation-independent high-throughput assessment of fungal biodiversity of an Amorphophallus species, and additionally expands the knowledge base on fungi associated with tea plants.
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11.
  • Keune, Hans, et al. (författare)
  • Defining Nature
  • 2022
  • Ingår i: Visseren-Hamakers, I., & Kok, M. (Eds.). (2022). Transforming Biodiversity Governance. Cambridge: Cambridge University Press.Transforming biodiversity governance. - Cambridge : Cambridge University Press. - 9781108856348 ; , s. 25-42
  • Bokkapitel (refereegranskat)
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12.
  • Tedersoo, Leho, et al. (författare)
  • Response to Comment on “Global diversity and geography of soil fungi”
  • 2015
  • Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 349:6251
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • Schadt and Rosling (Technical Comment, 26 June 2015, p. 1438) argue that primer-template mismatches neglected the fungal class Archaeorhizomycetes in a global soil survey. Amplicon-based metabarcoding of nine barcode-primer pair combinations and polymerase chain reaction (PCR)–free shotgun metagenomics revealed that barcode and primer choice and PCR bias drive the diversity and composition of microorganisms in general, but the Archaeorhizomycetes were little affected in the global study. We urge that careful choice of DNA markers and primers is essential for ecological studies using high-throughput sequencing for identification.
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13.
  • Némethy, Sándor, 1955, et al. (författare)
  • Collection, cultivation and processing of medical plants, herbs and spices in the Balaton Ecomuseum – herbal medicine as intangible cultural heritage
  • 2020
  • Ingår i: Ecocycles. - : Ecocycles. - 2416-2140. ; 6:1, s. 52-87
  • Tidskriftsartikel (refereegranskat)abstract
    • The Balaton Ecomuseum, which is being continuously developed since 2017, will have a holistic approach, where the objectives of the ecomuseum embrace the whole cultural landscape of Lake Balaton as one unit with several thematic routes in one system and shall not be restricted to one particular subject area or a part of local heritage. One of these thematic routes is the recently developingHerbs and Spices Network, led by Zánka Herb Valley Visitor and Training Centre based on the collection, cultivation and processing of medicinal plants, herbs and spices. The place of herbs and spices in the diet needs to be considered in reviewing health benefits, including definitions of the food category and the way in which benefits might be viewed, and therefore researched.Here we describe the already established system of the Zánka Herb Valley Visitor and Training Centre, the potential of the Balaton Region in the development of herbal medicine illustrated by the scientific presentation of the 30 most collected herbs in the region and examples of other herbal centres, which are intended to become a part of the network. Herbalmedicine, as an important part of the intangible cultural heritage, with hundreds of years old recipes for herbal concoctionshas been known since ancient times before science related to modern medicine developed and continues to be used for generationsuntil now. Furthermore, the medical effects of many agricultural crops should be better understood, such as the grapevine, which is being investigated for its medical compounds or the medicinal properties of other fruits and vegetables not sufficiently known to the general public. In this study we present a new system of the culture and interactive education of the collection, cultivation and use of medicinal plants, herbs and spices applying a learning by doing approach and a network embracing the whole area of the Balaton Ecomuseum.
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14.
  • Nilsson, R. Henrik, 1976, et al. (författare)
  • The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.
  • 2019
  • Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 47:D1
  • Tidskriftsartikel (refereegranskat)abstract
    • UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer(ITS) region-and offers all ∼1 000000 public fungal ITS sequences for reference. These are clustered into ∼459000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.
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15.
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16.
  • Tedersoo, Leho, et al. (författare)
  • Novel soil-inhabiting clades fill gaps in the fungal tree of life
  • 2017
  • Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • Background - Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water. Results - We provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH. Conclusions - This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
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17.
  • Biofuels, Land Grabbing and Food Security in Africa
  • 2011
  • Samlingsverk (redaktörskap) (refereegranskat)abstract
    • Energy crisis and climate change have generated global demands for alternative non-fossil fuel sources. This has led to a rapid increase of investments in production of liquid biofuels based on agricultural feed stocks such as sugar cane. Most African governments see biofuels as a potential for increasing agricultural productivity and export incomes and thus strengthening their national economies, improving energy balances and rural employment. At the same time climate change may be addressed through reduction of green house gas emissions.There are, however, a number of uncertainties mounting that challenge this scenario. Using in-depth African case studies this book addresses this knowledge gap by examining the impacts of large-scale biofuel production on African agriculture in regard to vital land outsourcing and food security issues. The surge for African biofuels has also opened space for private investors both domestic and external to multiply and network 'independently' of the state. The biofuel expansion thus generates new economic alliances and production relations, resulting in new forms of inclusions and exclusions within the rural population.An essential book for anyone wishing to understand the startling impact of biofuels and land outsourcing on Africa.
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18.
  • Hesselberg, Jan (författare)
  • The third world in transition : the case of the peasantry in Botswana
  • 1985
  • Bok (övrigt vetenskapligt/konstnärligt)abstract
    • The objective of the present work is through the case of Botswana to discuss the creation of poverty in the period of transition from tribal to modern society in the Third World today. This is done by an analysis focusing at the peasantry. The recently renewed fashion of blaming the peasants for lack of improved food production and thus for poverty at local and national levels is questioned.
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19.
  • Zanne, Amy E, et al. (författare)
  • Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.
  • 2020
  • Ingår i: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433
  • Tidskriftsartikel (refereegranskat)abstract
    • Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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20.
  • Elliott, David R., et al. (författare)
  • Bacterial and Fungal Communities in a Degraded Ombrotrophic Peatland Undergoing Natural and Managed Re-Vegetation
  • 2015
  • Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
  • Tidskriftsartikel (refereegranskat)abstract
    • The UK hosts 15–19% of global upland ombrotrophic (rain fed) peatlands that are estimated to store 3.2 billion tonnes of carbon and represent a critical upland habitat with regard to biodiversity and ecosystem services provision. Net production is dependent on an imbalance between growth of peat-forming Sphagnum mosses and microbial decomposition by microorganisms that are limited by cold, acidic, and anaerobic conditions. In the Southern Pennines, land-use change, drainage, and over 200 years of anthropogenic N and heavy metal deposition have contributed to severe peatland degradation manifested as a loss of vegetation leaving bare peat susceptible to erosion and deep gullying. A restoration programme designed to regain peat hydrology, stability and functionality has involved re-vegetation through nurse grass, dwarf shrub and Sphagnum re-introduction. Our aim was to characterise bacterial and fungal communities, via high-throughput rRNA gene sequencing, in the surface acrotelm/mesotelm of degraded bare peat, long-term stable vegetated peat, and natural and managed restorations. Compared to long-term vegetated areas the bare peat microbiome had significantly higher levels of oligotrophic marker phyla (Acidobacteria, Verrucomicrobia, TM6) and lower Bacteroidetes and Actinobacteria, together with much higher ligninolytic Basidiomycota. Fewer distinct microbial sequences and significantly fewer cultivable microbes were detected in bare peat compared to other areas. Microbial community structure was linked to restoration activity and correlated with soil edaphic variables (e.g. moisture and heavy metals). Although rapid community changes were evident following restoration activity, restored bare peat did not approach a similar microbial community structure to non-eroded areas even after 25 years, which may be related to the stabilisation of historic deposited heavy metals pollution in long-term stable areas. These primary findings are discussed in relation to bare peat oligotrophy, re-vegetation recalcitrance, rhizosphere-microbe-soil interactions, C, N and P cycling, trajectory of restoration, and ecosystem service implications for peatland restoration.
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21.
  • Barthel, Stephan, 1968-, et al. (författare)
  • Biocultural Refugia : Combating the Erosion of Diversity in Landscapes of Food Production
  • 2013
  • Ingår i: Ecology and Society. - 1708-3087. ; 18:4, s. UNSP 71-
  • Tidskriftsartikel (refereegranskat)abstract
    • There is urgent need to both reduce the rate of biodiversity loss caused by industrialized agriculture and feed morepeople. The aim of this paper is to highlight the role of places that harbor traditional ecological knowledge, artifacts, and methodswhen preserving biodiversity and ecosystem services in landscapes of food production. We use three examples in Europe ofbiocultural refugia, defined as the physical places that not only shelter farm biodiversity, but also carry knowledge and experiencesabout practical management of how to produce food while stewarding biodiversity and ecosystem services. Memory carriersinclude genotypes, landscape features, oral, and artistic traditions and self-organized systems of rules, and as such reflect adiverse portfolio of practices on how to deal with unpredictable change. We find that the rich biodiversity of many regionallydistinct cultural landscapes has been maintained through different smallholder practices developed in relation to localenvironmental fluctuations and carried within biocultural refugia for as long as millennia. Places that transmit traditionalecological knowledge and practices hold important lessons for policy makers since they may provide genetic and culturalreservoirs — refugia — for the wide array of species that have co-evolved with humans in Europe for more than 6000 thousandyrs. Biodiversity restoration projects in domesticated landscapes can employ the biophysical elements and cultural practicesembedded in biocultural refugia to create locally adapted small-scale mosaics of habitats that allow species to flourish and adaptto change. We conclude that such insights must be included in discussions of land-sparing vs. land-sharing when producingmore food while combating loss of biodiversity. We found the latter strategy rational in domesticated landscapes with a longhistory of agriculture
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22.
  • Green, Leon, et al. (författare)
  • Ancestral Sperm Ecotypes Reveal Multiple Invasions of a Non-Native Fish in Northern Europe
  • 2021
  • Ingår i: Cells. - : MDPI AG. - 2073-4409. ; 10:7
  • Tidskriftsartikel (refereegranskat)abstract
    • For externally fertilising organisms in the aquatic environment, the abiotic fertilisation medium can be a strong selecting force. Among bony fishes, sperm are adapted to function in a narrow salinity range. A notable exception is the family Gobiidae, where several species reproduce across a wide salinity range. The family also contains several wide-spread invasive species. To better understand how these fishes tolerate such varying conditions, we measured sperm performance in relation to salinity from a freshwater and a brackish population within their ancestral Ponto-Caspian region of the round goby, Neogobius melanostomus. These two ancestral populations were then compared to nine additional invaded sites across northern Europe, both in terms of their sperm traits and by using genomic SNP markers. Our results show clear patterns of ancestral adaptations to freshwater and brackish salinities in their sperm performance. Population genomic analyses show that the ancestral ecotypes have generally established themselves in environments that fit their sperm adaptations. Sites close to ports with intense shipping show that both outbreeding and admixture can affect the sperm performance of a population in a given salinity. Rapid adaptation to local conditions is also supported at some sites. Historical and contemporary evolution in the traits of the round goby sperm cells is tightly linked to the population and seascape genomics as well as biogeographic processes in these invasive fishes. Since the risk of a population establishing in an area is related to the genotype by environment match, port connectivity and the ancestry of the round goby population can likely be useful for predicting the species spread.
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23.
  • Ahrné, Karin, et al. (författare)
  • Tillstånd och trender för arter och deras livsmiljöer – rödlistade arter i Sverige 2015
  • 2015
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • 2015 års upplaga av den svenska rödlistan är den fjärde i ordningen. Den är baserad på IUCN:s rödlistningskriterier och revideras vart femte år. I rödlistan bedöms risken som enskilda arter av djur, växter och svampar löper att försvinna från Sverige. Bedömningen utförs av ArtDatabankens medarbetare i samverkan med över 100 externa experter, indelade i 14 expertkommittéer för olika organismgrupper. Under arbetet med 2015 års rödlista har tillstånd och trender bedömts för 21 600 arter och 1 318 lägre taxa (apomiktiska arter, underarter och varieteter), sammanlagt ca 22 900 taxa. Av de bedömda arterna klassificerades 2 029 som hotade (kategorierna CR, EN och VU) och 4 273 som rödlistade (inkluderar även kategorierna NT, RE och DD). Förhållandet mellan antalet rödlistade och antalet bedömda arter ar 19,8 %, vilket är ungefär samma värde som 2010 och 2005. I denna rapport jämförs antalet och andelen rödlistade arter mellan olika organismgrupper, biotoper, substrat och påverkansfaktorer. Texten ar indelad i en allmän del och åtta kapitel inriktade på olika landskapstyper. Landskapstyperna utgör en grov indelning av landets miljöer enligt följande kategorier: Skog, Jordbrukslandskap, Urbana miljöer, Fjäll, Våtmarker, Sötvatten, Havsstränder och Havsmiljöer. Skogen och jordbrukslandskapet är de artrikaste landskapstyperna med 1 800 respektive 1 400 arter som har en stark anknytning dit, och ytterligare flera hundra arter som förekommer där mer sporadiskt. De faktorer som påverkar flest rödlistade arter i Sverige är skogsavverkning och igenväxning, som båda utgör ett hot mot vardera ca 30 % av de rödlistade arterna. Avverkning minskar arealen av skog där naturliga strukturer och naturlig dynamik upprätthålls, och den orsakar därmed förlust av livsmiljöer. Igenväxning orsakas av ett antal faktorer, bland annat upphörande hävd (bete och slåtter), gödsling, trädplantering och brist på naturliga störningsregimer som t.ex. regelbundna översvämningar kring vattendrag och sjöar. Andra viktiga påverkansfaktorer är fiske, torrläggning av våtmarker, tillbakagång hos värdarter (främst alm och ask som drabbats av invasiva svampsjukdomar), klimatförändringar och konkurrens från invasiva arter. IUCN:s rödlisteindex beräknas för ett urval av de bedömda organismgrupperna. Rödlisteindex visar att skillnaderna mellan rödlistorna från 2000, 2005, 2010 och 2015 är små. Ett par undantag finns dock. Groddjur och stora däggdjur har fått en något förbättrad situation sedan 2000. Totalt förefaller det ändå som att trycket mot Sveriges artstock har förblivit relativt konstant under de senaste 15 åren.
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24.
  • Amundin, Mats, et al. (författare)
  • A proposal to use distributional models to analyse dolphin vocalisation
  • 2017
  • Ingår i: Proceedings of the 1st International Workshop on Vocal Interactivity in-and-between Humans, Animals and Robots, VIHAR 2017. - 9782956202905 ; , s. 31-32
  • Konferensbidrag (refereegranskat)abstract
    • This paper gives a brief introduction to the starting points of an experimental project to study dolphin communicative behaviour using distributional semantics, with methods implemented for the large scale study of human language.
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25.
  • Andersson, Erik, et al. (författare)
  • Ambio fit for the 2020s
  • 2022
  • Ingår i: Ambio. - : Springer Nature. - 0044-7447 .- 1654-7209. ; 51:5, s. 1091-1093
  • Tidskriftsartikel (refereegranskat)
  •  
26.
  • Macura, Biljana, et al. (författare)
  • What evidence exists on the effects of public policy interventions for achieving environmentally sustainable food consumption? : A systematic map protocol
  • 2022
  • Ingår i: Environmental Evidence. - : Springer Science and Business Media LLC. - 2047-2382. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The global food system is causing considerable environmental harm. A transition towards more sustainable consumption is needed. Targeted public policy interventions are crucial for stimulating such transition. While there is extensive research about the promotion of more environmentally sustainable food consumption, this knowledge is scattered across different sources. This systematic map aims to collate and describe the available evidence on public policy interventions such as laws, directives, taxes and information campaigns, for achieving sustainable food consumption patterns.Methods: We will search bibliographic databases, specialist websites, Google Scholar and bibliographies of relevant reviews. Searches for academic literature will be performed in English, while searches for grey literature will be performed in English, Swedish, Danish and Norwegian. Screening, including consistency checking exercises, will be done at two levels: title and abstract, and full text. We will use machine learning algorithms to support screening at the title and abstract level. Coding and meta-data extraction will include bibliographic information, policy details and context, and measured environmental outcome(s). The evidence base will be summarised narratively using tables and graphs and presented as an online interactive searchable database and a website that will allow for visualisation, filtering and exploring systematic map findings, knowledge gaps and clusters.
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27.
  • Unraveling the logics of landscape
  • 2014
  • Samlingsverk (redaktörskap) (övrigt vetenskapligt/konstnärligt)abstract
    • Despite conceptual oscillations through times, the concept of landscape remains highly subjective, whereupon unraveling its 'logics' opens up to a plurality of interpretations. Accordingly, by focusing on the interconnections present in the non-haphazard production of landscape, this publication elaborates on how the rural landscape is valued, monitored, changed, harbored, used and misused, be it through actions, representations or metaphors. This book covers a broad range of topics, with contributions from scholars from more than 30 countries.
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28.
  • Ran, Ylva, et al. (författare)
  • Effects of public policy interventions for environmentally sustainable food consumption: a systematic map of available evidence
  • 2024
  • Ingår i: Environmental Evidence. - 2047-2382. ; 13
  • Forskningsöversikt (refereegranskat)abstract
    • Background The global food system is inflicting substantial environmental harm, necessitating a shift towards more environmentally sustainable food consumption practices. Policy interventions, for example, information campaigns, taxes and subsidies and changes in the choice context are essential to stimulate sustainable change, but their effectiveness in achieving environmental goals remains inadequately understood. Existing literature lacks a comprehensive synthesis of evidence on the role of public policies in promoting sustainable food consumption. Our systematic map addressed this gap by collecting and categorising research evidence on public policy interventions aimed at establishing environmentally sustainable food consumption patterns, in order to answer the primary research question: What evidence exists on the effects of public policy interventions for achieving environmentally sustainable food consumption?Methods Searches for relevant records (in English) were performed in WoS, Scopus, ASSIA, ProQuest Dissertation and Theses, EconLit, Google Scholar and in bibliographies of relevant reviews. A grey literature search was also performed on 28 specialist websites (searches were made in the original language of the webpages and publications in English, Swedish, Danish and Norwegian were eligible) and Google Scholar (search in English). Screening was performed at title/abstract and full-text levels, with machine learning-aided priority screening at title/abstract level. Eligibility criteria encompassed settings, interventions (public policies on sustainable food consumption), target groups and outcomes. No critical appraisal of study validity was conducted. Data coding covered bibliographic details, study characteristics, intervention types and outcomes. Evidence was categorised into intervention types and subcategories. Visual representation utilised bar plots, diagrams, heatmaps and an evidence atlas. This produced a comprehensive overview of effects of public policy interventions on sustainable food consumption patterns.Review findings The evidence base included 227 articles (267 interventions), with 92% of studies in high-income countries and only 4% in low-income countries. Quantitative studies dominated (83%), followed by mixed methods (16%) and qualitative studies (1%). Most interventions were information-based and 50% of reviewed studies looked at labels. Information campaigns/education interventions constituted 10% of the sample, and menu design changes and restriction/editing of choice context 8% each. Market-based interventions represented 13% of total interventions, of which two-thirds were taxes. Administrative interventions were rare (< 1%). Proxies for environmental impact (85%) were more frequent outcome measures than direct impacts (15%). Animal-source food consumption was commonly used (19%) for effects of interventions on, for example, greenhouse gas emissions. Most studies used stated preferences (61%) to evaluate interventions.Conclusions The literature assessing policies for sustainable food consumption is dominated by studies on non-intrusive policy instruments; labels, information campaigns, menu design changes and editing choice contexts. There is a strong need for research on sustainable food policies to leave the lab and enter the real world, which will require support and cooperation of public and private sector stakeholders. Impact evaluations of large-scale interventions require scaling-up of available research funding and stronger multidisciplinary research, including collaborations with industry and other societal actors. Future research in this field should also go beyond the European and North American context, to obtain evidence on how to counteract increasing environmental pressures from food consumption worldwide.
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29.
  • Sonesten, Lars (författare)
  • Miljöövervakningen av Sveriges sjöar och vattendrag : Representativiteten av den kontrollerande miljöövervakningen
  • 2013
  • 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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30.
  • Lindborg, Regina, et al. (författare)
  • Investigating biodiversity trajectories using scenarios – Lessons from two contrasting agricultural landscapes
  • 2009
  • Ingår i: Journal of Environmental Management. - : Elsevier BV. - 0301-4797 .- 1095-8630. ; 91:2, s. 499-508
  • Tidskriftsartikel (refereegranskat)abstract
    • Agriculture is the major land use at a global scale. In addition to food production, multifunctionality of landscapes, including values and ecosystem services like biodiversity, recreation and culture, is now focus for management. This study explores how a scenario approach, involving different stakeholders, may help to improve landscape management for biodiversity conservation. Local farmers and executives at the County Administrative Board were invited to discuss rural development and conditions for farmland biodiversity in two Swedish landscapes. The potential biodiversity for three future land use scenarios for the two landscapes was discussed: nature conservation, outdoor recreation and energy production, and compared with current and historical landscapes in each region. Analyses of habitat areas, connectedness and landscape diversity suggested that the energy and recreation scenarios had a negative impact on farmland biodiversity, whereas the nature conservation scenario, the current and historically reconstructed landscapes had a higher potential for biodiversity. The farmers appreciated the nature conservation scenario, but also the energy production scenario and they highlighted the need of increased subsidies for management of biodiversity. The farmers in the high production area were less interested in nature quality per se. The executives had similar opinions as the farmers, but disagreed on the advantages with energy production, as this would be in conflict with the high biodiversity and recreational values. The local physical and socio-economical conditions differ between landscapes and potentially shaped the stakeholders emotional attachment to the local environment, their opinions and decisions on how to manage the land. We stress the importance of incorporating local knowledge, visions and regional prerequisites for different land uses in conservation, since site and landscape specific planning for biodiversity together with a flexible subsidy system are necessary to reach the conservation goals within EU.
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31.
  • Abarenkov, Kessy, et al. (författare)
  • Protax-fungi: A web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences
  • 2018
  • Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 220:2, s. 517-525
  • Tidskriftsartikel (refereegranskat)abstract
    • © 2018 New Phytologist Trust. Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax-fungi, a general tool for taxonomic placement of fungal internal transcribed spacer (ITS) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. With empirical data on root- and wood-associated fungi, Protax-fungi reliably identified (with at least 90% identification probability) the majority of sequences to the order level but only around one-fifth of them to the species level, reflecting the current limited coverage of the databases. Protax-fungi outperformed the Sintax and Rdb classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. We applied Protax-fungi to examine the internal consistencies of the Index Fungorum and UNITE databases. This revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. Protax-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships.
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32.
  • Ode Sang, Åsa, et al. (författare)
  • The effects of naturalness, gender, and age on how urban green space is perceived and used
  • 2016
  • Ingår i: Urban Forestry & Urban Greening. - : Elsevier BV. - 1618-8667 .- 1610-8167. ; 18, s. 268-276
  • Tidskriftsartikel (refereegranskat)abstract
    • Neighbourhood green space serves an important function for the urban population, and provides valuable ecosystem services for human well-being. In this article, we investigate the effects of naturalness, gender, and age on the activities, aesthetics, and self-reported well-being associated with urban green space. Our findings are based on a postal survey of residents living in close proximity to six different green spaces in the city of Gothenburg, Sweden. It is shown that higher perceived naturalness generated more activities and higher aesthetic values and self-reported well-being for residents living close to urban green spaces. The results also indicated that, regardless of the type of naturalness, women were more active in urban green spaces than were men. Women also saw greater aesthetic value in green spaces than men did, and had higher self-reported well-being associated with the urban green spaces. Finally, older residents were shown to participate in a greater number of nature-related activities than younger residents. Older residents also saw greater aesthetic values and had higher self-reported well-being associated with urban green spaces than younger people did. Seemingly, this poses a considerable planning challenge if areas of perceived naturalness are to be retained in cities, since the present trend is for reduced green spaces in cities and a ‘parkification’ of surviving natural areas. Further, because of the importance of perceived natural areas to the elderly, and in particularly women, distances to urban green areas should not be too great.
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33.
  • Tedersoo, Leho, et al. (författare)
  • Standardizing metadata and taxonomic identification in metabarcoding studies
  • 2015
  • Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X .- 2047-217X. ; 4
  • Tidskriftsartikel (refereegranskat)abstract
    • High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.
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34.
  • Vitalis Pemunta, Ngambouk, 1973, et al. (författare)
  • Modern State Law: Regulating Tradition or Protecting the Environment in the Mankon Kingdom of Northwest Cameroon?
  • 2019
  • Ingår i: Endemic Species. Eusebio Cano Carmona (red.). - London, United Kingdom : Intechopen. - 9781839623547
  • Bokkapitel (refereegranskat)abstract
    • Most African countries including Cameroon find themselves in a situation of legal pluralism and at crossroads with implications for the sustainable management of natural resources. Traditional institutions and knowledge systems have been hailed as invaluable mechanisms for the conservation of flora and fauna. This chapter examines the conflict between traditional institutions and State law in the hierarchically stratified Mankon Kingdom of the Grassfield region of Northwest Cameroon where the latter prohibits the harvesting of culturally valuable plant and animal species for myriad ritual ceremonies and for therapeutic purposes. It demonstrates that the lack of cultural sensitivity can be antithetical to conservation initiatives. In other words, there is the need to align current legislative regulations for the management of natural species with the traditional use of territory, gender roles as well as to raise the cultural and educational level of the population through sensitization on the need to conserve the natural environment on which their culture depends for its survival.
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35.
  • Nilsson, R. Henrik, 1976, et al. (författare)
  • Improving ITS sequence data for identification of plant pathogenic fungi
  • 2014
  • Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 67:1, s. 11-19
  • Tidskriftsartikel (refereegranskat)abstract
    • Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.
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36.
  • Schoch, Conrad L., et al. (författare)
  • Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
  • 2014
  • Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
  • Tidskriftsartikel (refereegranskat)abstract
    • DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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37.
  • kaiser, matthias, et al. (författare)
  • Food ethics: a Wide Field in Need of Dialogue
  • 2016
  • Ingår i: Food Ethics. - : Springer Science and Business Media LLC. - 2364-6853 .- 2364-6861. ; 1:1, s. 1-7
  • Tidskriftsartikel (refereegranskat)abstract
    • There are a few things which are obviously a central part of everyone’s life, at all times, and all over the globe, and which are crucial for our wellbeing. Food is, like sex, such an essential ingredient of our life, an ingredient of what we expect of a good life. What is on our plates is always a result of nature and culture, to the extent that it may seem hard to find commonalities in our global diet. As academics we have asked different questions about food. For a long time these questions have been dominated by the quest to secure enough food and to improve what we have got. It is, however, noteworthy that we also always have asked the normative questions in relation to food: Is it right to eat this kind of food? Do we produce our food the right way? Is there injustice and bad power in the way we distribute the food? Are we lied to in regard to what is on our plate? When we enter the normative realm, we enter the realm of ethics, understood in a wide and comprehensive way. As all normative questions, we need to be well informed by knowledge about how the world is, and what is at stake and for whom. We call this food ethics. Food ethics raises issues and asks questions in relation to food all along the value chains. It also puts things into relation with each other. At the same time it disentangles complex heaps of factors and pieces of knowledge, and looks for guidance. It is issue driven, rather than interest driven. It unites scholars with farmers and fishermen, chefs with industry, consumers with lawyers, and food citizens with authorities. As a young field within academia it is important to guard against efforts to appropriate the field for narrow interests, and instead to combine the natural and social sciences in analysing and addressing the challenges. We do not necessarily call for the grand ethical theory that explains it all, but rather start with the simple things in a very complex overall picture. We want to draw attention to ethically significant facts, discuss problematic developments, point to genuine dilemmas, learn about food relevant contexts and history, and look for individual, professional and institutional responses to ethical challenges and issues. Thus, one of the missions of this new journal Food Ethics, is to widen the scope and the discussion on the topic, and to be inclusive in terms of who has something to contribute to the field. There is no escaping from confronting very complex issues when it comes to managing one of the most basic needs we all have, food. As editors of this new journal we maintain that food ethics deserves special and inter-disciplinary attention by researchers, that it is not sufficiently dealt with by what is currently known as bioethics, that it is intrinsically connected with the so-called grand societal challenges of our time, that it is a globally important field which demands particular attention to complexities and uncertainties, as much as it needs to be explicit about what values are at stake and for whom, and which normative principles it touches upon.
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38.
  • Lind, Lovisa, et al. (författare)
  • Towards ecologically functional riparian zones : A meta-analysis to develop guidelines for protecting ecosystem functions and biodiversity in agricultural landscapes
  • 2019
  • Ingår i: Journal of Environmental Management. - London : Academic Press. - 0301-4797 .- 1095-8630. ; 249, s. 1-8
  • Tidskriftsartikel (refereegranskat)abstract
    • Riparian zones contribute with biodiversity and ecosystem functions of fundamental importance for regulating flow and nutrient transport in waterways. However, agricultural land-use and physical changes made to improve crop productivity and yield have resulted in modified hydrology and displaced natural vegetation. The modification to the hydrology and natural vegetation have affected the biodiversity and many ecosystem functions provided by riparian zones. Here we review the literature to provide state-of-the-art recommendations for riparian zones in agricultural landscapes. We analysed all available publications since 1984 that have quantified services provided by riparian zones and use this information to recommend minimum buffer widths. We also analysed publications that gave buffer width recommendations to sustain different groups of organisms. We found that drainage size matters for nutrient and sediment removal, but also that a 3 m wide buffer zone acts as a basic nutrient filter. However, to maintain a high floral diversity, a 24 m buffer zone is required, while a 144 m buffer is needed to preserve bird diversity. Based on the analysis, we developed the concept of “Ecologically Functional Riparian Zones” (ERZ) and provide a step-by-step framework that managers can use to balance agricultural needs and environmental protection of waterways from negative impacts. By applying ERZ in already existing agricultural areas, we can better meet small targets and move towards the long-term goal of achieving a more functional land management and better environmental status of waterways.
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39.
  • Tedersoo, Leho, et al. (författare)
  • Global patterns in endemicity and vulnerability of soil fungi.
  • 2022
  • Ingår i: Global change biology. - : Wiley. - 1365-2486 .- 1354-1013. ; 28:22, s. 6696-6710
  • Tidskriftsartikel (refereegranskat)abstract
    • Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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40.
  • Strong, Emily A., et al. (författare)
  • Seeking greener pastures : crop selection by Greylag Geese (Anser anser) during the moulting season
  • 2021
  • Ingår i: Ornis Fennica. - : Finnish Omithological Soc. - 0030-5685. ; 98:1, s. 16-32
  • Tidskriftsartikel (refereegranskat)abstract
    • Over the last 40 years, many goose populations have recovered from historic lows and are now more numerous than ever. At the same time, geese have shifted from natural foraging habitats to securing most of their nutritional demands from agricultural fields, leading to crop damage and conflict with agriculture. We studied field use by Greylag Geese (Anser anser) in the agricultural landscape surrounding a main breeding and moulting lake in Sweden. From 2012 to 2016, weekly roadside surveys were conducted from May to July. Data were collected on goose numbers, crop type and sward height in agricultural fields. Using a compositional analysis, we demonstrate that Greylag Geese show a strong selection for ley and pasture fields compared to other crop types (rank order: ley/pasture > oat > barley > wheat > other crops). This selection was consistent across years and between pre- and post-moult. Aside from ley and pasture, no other croptypes were selected for, as they were used less than expected given their availability. Irrespective of crop type, geese foraged predominantly on short (0–10 cm) swards. The strong selection for ley and pasture may have been driven by higher nutritional quality of short, managed grass swards relative to other available foods. This suggests that during the summer grass fields may be more vulnerable to damage compared to other crop types. Our study provides a deeper understanding of the ecology of Greylag Geese, which may be used to inform management strategies focused on mitigating crop damage and alleviating conflict.
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41.
  • Hyde, Kevin D., et al. (författare)
  • Incorporating molecular data in fungal systematics: a guide for aspiring researchers
  • 2013
  • Ingår i: Current Research in Environmental and Applied Mycology. - : Mushroom Research Foundation. - 2229-2225. ; 3:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.
  •  
42.
  • Beyene, Atakilte (författare)
  • Costly not to consider local resistance : Advice on agricultural investments in Africa
  • 2013
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • Failures in considering and properly addressing local resistance have become costly for both the local people and the investors. Land acquisition policies need to be accompanied by mechanisms that address local grievances and conflicts. These aspects are crucial not only to alleviate unjust practices, but also to enhance confidence of investors and performance of the investments.
  •  
43.
  • Tedersoo, Leho, et al. (författare)
  • Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi
  • 2015
  • Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 10, s. 1-43
  • Tidskriftsartikel (refereegranskat)abstract
    • Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6–38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.
  •  
44.
  • Öhrman, Phillip, et al. (författare)
  • En studie om tillit till inventeringssystemet för stora rovdjur
  • 2019
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • Tillit, att lita på samhället och på sina medmänniskor, är samhällets kitt. Ett samhälle, inklusive dess olika komponenter, som präglas av hög tillit antas fungera bättre än om tilliten är låg. Syftet med vår studie är att utvärdera tilliten till inventeringssystemet för stora rovdjur bland de myndigheter och intresseorganisationer som är direkt berörda av systemet. På basis av intervjuer utvärderade vi tilliten genom sex olika delkomponenter; kommunikation,ansvars- och kompetensfördelning, resurser, respekt, kunskap och rättvisa. Vi har identifierat brister i alla sex delkomponenterna vilket sammantaget resulterar i att tilliten för systemet kan betecknas som låg. • Kommunikationen i systemet; hur kommunikationen sker, vad somkommuniceras, och på vilket sätt beslut kommuniceras upplevs som undermålig.• Ansvars- och kompetensfördelningen upplevs som otydlig. Det finns en klyfta mellan de som fastställer regler och riktlinjer och de som utför inventeringarna, varför relationerna präglas mer av kontroll och misstro än av handlingsutrymme och tillit.• Inventeringsresurserna räcker inte till eller prioriteras fel; t.ex. prioriteras varg på bekostnad av de övriga arterna. Det minskar förutsättningarna att fatta välgrundade beslut om ersättningar för rovdjurspredation ochom licens- och skyddsjakt.• Respekten för kunskap, näringsverksamhet och ideellt arbete upplevs som bristfällig. Respekten missgynnas också av den rigida kontrollkultur som upplevs ha utvecklats till följd av mål- och resultatstyrning i kombination med strikta inventeringskriterier.• Integrationen av ny kunskap är bristfällig. Bristen på ett systematiskt s.k. adaptivt lärande leder till att nya lösningar inte tillämpas eller utvecklas i tillräckligt hög grad.• Systemet upplevs som orättvist och slutet. En översyn av hur kostnader och nytta fördelas efterlyses av aktörerna, både vad gäller direkta kostnader,men även transaktionskostnader, dvs. kostnader förknippade med samråd och samverkan. Det är också oklart hur aktörerna aktivt tillåts delta i utvecklingen av systemet. Aktörerna lyfter fram en rad förslag till hur tilliten kan stärkas. Det utgör grunden till förbättringar som också kan accepteras av de flesta:• Inled ett systematiskt kvalitetssäkringsarbete med fokus på dialog och aktörssamverkan, till exempel inom ramen för Dialog för Naturvård.• Arbeta gemensamt fram en tydlig rollfördelning som beskriver vem som gör vad, när och varför inom hela inventeringskedjan, med syftet att öka förutsägbarheten för alla inblandade.• Skapa incitament och strukturer för adaptiv förvaltning inom hela inventeringskedjan,på alla nivåer.• Ta fram en översyn av hur kostnader och nytta fördelas för alla aktörer.Det ska inkludera direkta kostnader och transaktionskostnader, dvs. kostnader förknippade med samråd och samverkan.• Utveckla och effektivisera inventeringsmetoderna, gärna med ny teknik som DNA, kameror och drönare. Utöka samarbetet med forskningsprojekt som till exempel ScandCam.• Återkoppla direkt till intresseorganisationernas och allmänhetens observationerför att öka motivationen att rapportera.• Utveckla ett regelverk för de år där det saknas inventeringsdata (t.ex.på grund av snöbrist), genom till exempel en rutin för framskrivning av antalet djur baserat på trendanalys.• Minska fjärrstyrningen, NVs roll bör vara mer koordinerande än kontrollerande.• Verka för kunskapsintegration (s.k. kollektiv intelligens) genom att samordnakunskaper, vetenskaplig samt lokal och traditionell kunskap, så att det gagnar hela systemet.• Gör en översyn av hur resurser fördelas och prioriteras i systemet.
  •  
45.
  • Blennow, Kristina, et al. (författare)
  • Societal impacts of storm damage
  • 2013
  • Ingår i: Living with Storm Damage to Forests. What science can tell us. - 9789525980097 ; :3, s. 70-77
  • Bokkapitel (övrigt vetenskapligt/konstnärligt)
  •  
46.
  • Johansson, Maria, et al. (författare)
  • Factors governing human fear of wolves : moderating effects of geographical location and standpoint on protected nature
  • 2016
  • Ingår i: European Journal of Wildlife Research. - New York : Springer. - 1612-4642 .- 1439-0574. ; 62:6, s. 749-760
  • Tidskriftsartikel (refereegranskat)abstract
    • This study analyses psychological antecedents of feelings of fear of wolves in a proportional sample of the Swedish population (national sample, n = 545) and in a sample of people in counties with wolf presence (regional sample, n = 1,892). Structural equation modelling of survey data suggests a dual pathway to self-reported fear. One path encompasses the appraisal of the environmental context operationalised as a potential wolf encounter. The second path concerns the appraisal of the social context assessed as social trust in managing authorities. The relative importance of the paths differs between the national and the regional sample, and between people in the administrative centre of the region and the regional periphery. We show that the public's fear of wolves should be addressed both at an individual level, focusing on situations with potential encounters, and at a collective level, by strengthening the trust between the public and authorities, and regional variation should be considered.
  •  
47.
  • Kerekes, Jennifer, et al. (författare)
  • Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest
  • 2013
  • Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 22:10, s. 2827-2838
  • Tidskriftsartikel (refereegranskat)abstract
    • Microbial communities play a major role in terrestrial ecosystem functioning, but the determinates of their diversity and functional interactions are not well known. In this study, we explored leaf litter fungal diversity in a diverse Panama lowland tropical forest in which a replicated factorial N, P, K and micronutrient fertilization experiment of 40 × 40 m plots had been ongoing for nine years. We extracted DNA from leaf litter samples and used fungal-specific amplification and a 454 pyrosequencing approach to sequence two loci, the nuclear ribosomal internal transcribed spacer (ITS) region and the nuclear ribosomal large subunit (LSU) D1 region. Using a 95% sequence similarity threshold for ITS1 spacer recovered a total of 2523 OTUs, and the number of unique ITS1 OTUs per 0.5–1.0 g leaf litter sample ranged from 55 to 177. Ascomycota were the dominant phylum among the leaf litter fungi (71% of the OTUs), followed by Basidiomycota (26% of the OTUs). In contrast to our expectations based on temperate ecosystems, long-term addition of nutrients increased, rather than decreased, species richness relative to controls. Effect of individual nutrients was more subtle and seen primarily as changes in community compositions especially at lower taxonomic levels, rather than as significant changes in species richness. For example, plots receiving P tended to show a greater similarity in community composition compared to the other nutrient treatments, the +PK, +NK and +NPK plots appeared to be more dominated by the Nectriaceae than other treatments, and indicator species for particular nutrient combinations were identified.
  •  
48.
  • Nilsson, R. Henrik, 1976 (författare)
  • Unifying fungi
  • 2015
  • Ingår i: Science & Technology. - 2049-2391 .- 2049-2405. ; :14, s. 204-206
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
  •  
49.
  • Ode Sang, Åsa, et al. (författare)
  • Are path choices of people moving through urban green spaces explained by gender and age? Implications for planning and management
  • 2020
  • Ingår i: Urban Forestry & Urban Greening. - : Elsevier BV. - 1618-8667 .- 1610-8167. ; 49
  • Tidskriftsartikel (refereegranskat)abstract
    • Neighbourhood green space is an important asset for the urban population, providing valuable ecosystem services such as supporting human health. Distance or access to urban green areas is well established as being important for the potential use of the area but how different demographic groups move within greenspace is still somewhat unknown. Previous studies have shown that there are gender as well as age differences in visual perception, audio experience and recreational activities as well as estimated well-being experienced from use of urban green space. Here we explored people's movement within their local green space in the city of Gothenburg, Sweden. The results showed that movement took place over large parts of the green spaces studied, not only along paths. The data further showed that the movement pattern differed significantly between men and women as well as between young adults and old adults. Movement patterns of demographic groups could provide support to planning for sustainable urban green areas, help avoid conflict, identify areas for solitude and ensure equal access for people of different gender and age.
  •  
50.
  •  
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