1. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Mycobiome diversity: high-throughput sequencing and identification of fungi.
- 2019
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In: Nature reviews. Microbiology. - : Springer Science and Business Media LLC. - 1740-1534 .- 1740-1526. ; 17, s. 95-109
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Research review (peer-reviewed)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.
(author)
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A price tag on species
- 2022
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In: Research Ideas and Outcomes_RIO. - : Pensoft Publishers. - 2367-7163. ; 8, s. 1-7
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Journal article (peer-reviewed)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. |
- Abarenkov, Kessy, et al.
(author)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Journal article (peer-reviewed)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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4. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms
- 2022
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In: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 239-244
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Journal article (peer-reviewed)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. |
- Sigvald, Roland, et al.
(author)
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Molecular identification of bloodmeals and species composition in Culicoides biting midges
- 2013
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In: Medical and Veterinary Entomology. - : Wiley. - 0269-283X .- 1365-2915. ; 27, s. 104-112
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Journal article (peer-reviewed)abstract
- Investigations of host preferences in haematophagous insects, including Culicoides biting midges (Diptera: Ceratopogonidae), are critical in order to assess transmission routes of vector-borne diseases. In this study, we collected and morphologically identified 164 blood-engorged Culicoides females caught in both light traps and permanent 12-m high suction traps during 20082010 in Sweden. Molecular analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene in the biting midges was performed to verify species classification, discern phylogenetic relationships and uncover possible cryptic species. Bloodmeal analysis using universal vertebrate cytochrome b primers revealed a clear distinction in host selection between mammalophilic and ornithophilic Culicoides species. Host sequences found matches in horse (n = 59), sheep (n = 39), cattle (n = 26), Eurasian elk (n = 1) and 10 different bird species (n = 18). We identified 15 Culicoides species previously recorded in Scandinavia and four additional species haplotypes that were distinctly different from the described species. All ornithophilic individuals (n = 23) were caught exclusively in the suction traps, as were, interestingly, almost all mammalophilic species (n = 41), indicating that many biting midge species may be able to cover long distances after completing a bloodmeal. These results add new information on the composition of Culicoides species and their host preferences and their potential long-distance dispersal while blood-engorged.
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6. |
- Alm Rosenblad, Magnus, 1957, et al.
(author)
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Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)
- 2016
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 13, s. 21-33
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Journal article (peer-reviewed)abstract
- During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.
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7. |
- Radek, Renate, et al.
(author)
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Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota
- 2017
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 25, s. 31-50
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Journal article (peer-reviewed)abstract
- Nephridiophagids are poorly known unicellular eukaryotes, previously of uncertain systematic position, that parasitize the Malpighian tubules of insects. Their life cycle includes merogony with multinucleate plasmodia and sporogony leading to small, uninucleate spores. We examined the phylogenetic affiliations of three species of Nephridiophaga, including one new species, Nephridiophaga maderae, from the Madeira cockroach (Leucophaea maderae). In addition to the specific host, the new species differs from those already known by the size of the spores and by the number of spores within the sporogenic plasmodium. The inferred phylogenetic analyses strongly support a placement of the nephridiophagids in the fungal kingdom near its root and with a close, but unresolved, relationship to the chytids (Chytridiomycota). We found evidence for the nephridiophagidean speciation as being strongly coupled to host speciation.
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8. |
- Unterseher, Martin, et al.
(author)
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Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition
- 2018
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In: Mycological Progress. - : Springer Science and Business Media LLC. - 1617-416X .- 1861-8952. ; 17:4, s. 489-500
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Journal article (peer-reviewed)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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9. |
- Ritter, Camila, et al.
(author)
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The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia
- 2019
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
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Journal article (peer-reviewed)abstract
- © 2019, The Author(s). Most knowledge on biodiversity derives from the study of charismatic macro-organisms, such as birds and trees. However, the diversity of micro-organisms constitutes the majority of all life forms on Earth. Here, we ask if the patterns of richness inferred for macro-organisms are similar for micro-organisms. For this, we barcoded samples of soil, litter and insects from four localities on a west-to-east transect across Amazonia. We quantified richness as Operational Taxonomic Units (OTUs) in those samples using three molecular markers. We then compared OTU richness with species richness of two relatively well-studied organism groups in Amazonia: trees and birds. We find that OTU richness shows a declining west-to-east diversity gradient that is in agreement with the species richness patterns documented here and previously for birds and trees. These results suggest that most taxonomic groups respond to the same overall diversity gradients at large spatial scales. However, our results show a different pattern of richness in relation to habitat types, suggesting that the idiosyncrasies of each taxonomic group and peculiarities of the local environment frequently override large-scale diversity gradients. Our findings caution against using the diversity distribution of one taxonomic group as an indication of patterns of richness across all groups.
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10. |
- Zanne, Amy E, et al.
(author)
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Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.
- 2020
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In: Biological reviews of the Cambridge Philosophical Society. - : Wiley. - 1469-185X .- 1464-7931. ; 95:2, s. 409-433
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Journal article (peer-reviewed)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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