| 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. |
- Kõljalg, Urmas, et al.
(författare)
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A price tag on species
- 2022
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Ingår i: Research Ideas and Outcomes_RIO. - : Pensoft Publishers. - 2367-7163. ; 8, s. 1-7
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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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| 3. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms
- 2022
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Ingår i: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6
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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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| 4. |
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| 5. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
- 2018
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Ingår i: Bioinformatics (Oxford, England). - : Oxford University Press (OUP). - 1367-4811 .- 1367-4803. ; 34:23
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Tidskriftsartikel (refereegranskat)abstract
- Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.We evaluated the Metaxa2 Database Builder on eleven commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.Supplementary data are available at Bioinformatics online.
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| 6. |
- Berglund, Fanny, et al.
(författare)
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Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge
- 2023
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where such initial mobilization events of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes.
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| 7. |
- Zanne, Amy E, et al.
(författare)
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Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.
- 2020
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Ingår i: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433
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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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| 8. |
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| 9. |
- Andersson, Martin O., et al.
(författare)
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Molecular detection of Babesia capreoli and Babesia venatorum in wild Swedish roe deer, Capreolus capreolus
- 2016
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Ingår i: Parasites & Vectors. - : Springer Science and Business Media LLC. - 1756-3305. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The epidemiology of the zoonotic tick-transmitted parasite Babesia spp. and its occurrence in wild reservoir hosts in Sweden is unclear. In European deer, several parasite species, including Babesia capreoli and the zoonotic B. venatorum and B. divergens has been reported previously. The European roe deer, Capreolus capreolus, is an important and common part of the indigenous fauna in Europe, as well as an important host for Ixodes ricinus ticks, the vector of several Babesia spp. in Europe. Here, we aimed to investigate the occurrence of Babesia spp. in roe deer in Sweden. Findings: Roe deer (n = 77) were caught and sampled for blood. Babesia spp. was detected with a PCR assay targeting the 18S rRNA gene. The prevalence of Babesia spp. was 52 %, and two species were detected; B. capreoli and B. venatorum in 44 and 7.8 % of the individuals, respectively. Infection occurred both in summer and winter. Conclusions: We showed that roe deer in Sweden, close to the edge of their northern inland distributional range, are infected with Babesia spp. The occurrence of B. venatorum in roe deer imply that it is established in Sweden and the zoonotic implication of this finding should be regarded to a greater extent in future.
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| 10. |
- Lisney, Thomas J., et al.
(författare)
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Using electroretinograms to assess flicker fusion frequency in domestic hens Gallus gallus domesticus
- 2012
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Ingår i: Vision Research. - : Elsevier BV. - 0042-6989 .- 1878-5646. ; 62, s. 125-133
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Tidskriftsartikel (refereegranskat)abstract
- The assessment of flicker fusion frequency (FFF), the stimulus frequency at which a flickering light stimulus can no longer be resolved and appears continuous, and critical flicker fusion frequency (CFF; the highest frequency at any light intensity that an observer can resolve flicker) are useful methods for comparing temporal resolution capabilities between animals. Behavioural experiments have found that average CFFs in domestic chickens (Gallus gallus domesticus) are in the range of ca. 75-87 Hz, measured in response to full spectrum (i.e. white light plus UV) stimuli. In order to examine whether the chicken retina is able to detect flicker at higher frequencies, we used electroretinograms (ERGs) to assess FFF/CFF in adult hens from two commercial genotypes, Lohmann Selected Leghorns (LSLs) and Lohmann Browns (LBs). ERGs were recorded in response to flickering light at ten full spectrum light intensities ranging from 0.7 to 2740 cd m(-2). Two methods were used to determine FFF/CFF from the ERG recordings and these methods yielded very similar results, with average FFF ranging from ca. 20 Hz at 0.7 cd m(-2) to an average CFF of ca. 105 Hz at 2740 cd m(-2). In some individuals, CFFs of 118-119 Hz were recorded. The Intensity/FFF (I/FFF) curves are double-branched with a break point representing the rod-cone transition occurring between 2.5 and 5.9 cd m(-2). No significant differences in the I/FFF curves were found between the two genotypes. At stimulus light intensities >250 cd m(-2), the ERG-derived FFF and CFF values are all higher than those from behavioural studies using the same stimuli. Although hens do not appear to be able to consciously perceive flicker above approximately 90 Hz, the finding that the ERG responses are able to remain in phase with light flickering at frequencies >100 Hz means that the retinae of domestic poultry housed in artificial light conditions may be able to resolve flicker from fluorescent lamps. As range of detrimental effects have been reported in humans as a result of exposure to such "invisible flicker", the possibility exists that flicker from fluorescent lamps also acts as stressor in domesticated birds.
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