| 51. |
- Phukhamsakda, Chayanard, et al.
(författare)
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The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding
- 2022
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Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 114:1, s. 327-386
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Tidskriftsartikel (refereegranskat)abstract
- The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.
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| 52. |
- Tedersoo, Leho, et al.
(författare)
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EUKARYOME: the rRNA gene reference database for identification of all eukaryotes
- 2024
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Ingår i: Database. - 1758-0463. ; 2024
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Tidskriftsartikel (refereegranskat)abstract
- Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers - ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding - a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.
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| 53. |
- Tedersoo, Leho, et al.
(författare)
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Global patterns in endemicity and vulnerability of soil fungi.
- 2022
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Ingår i: Global change biology. - : Wiley. - 1365-2486 .- 1354-1013. ; 28:22, s. 6696-6710
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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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| 54. |
- Tedersoo, Leho, et al.
(författare)
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Response to Comment on “Global diversity and geography of soil fungi”
- 2015
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 349:6251
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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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| 55. |
- Wurzbacher, Christian, 1980, et al.
(författare)
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Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.
- 2017
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Ingår i: The ISME journal. - : Springer Science and Business Media LLC. - 1751-7370 .- 1751-7362. ; 11:8, s. 1938-1941
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Tidskriftsartikel (refereegranskat)abstract
- In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.
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| 56. |
- Janzon, Anders, 1978, et al.
(författare)
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Exploring the microbial resistome in river sediments exposed to extraordinary high levels of antibiotics
- 2010
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Ingår i: 35th FEBS Congress: Molecules of Life.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The rapid development and propagation of antibiotic resistance in pathogenic and opportunistic bacteria is a major threat to public health worldwide. The phenomenon has been widely studied in the clinical setting, but comparatively little is known about the prevalence and diversity of antibiotic resistance in communities of environmental bacteria, often referred to as the environmental resistome. As the external environment may function as a reservoir of resistance genes to human pathogens, we are interested in how environmental bacteria are affected by antibiotic pollution. We have previously isolated microbial DNA from river sediments taken up- and downstream from a water treatment plant that processes waste water from several pharmaceutical plants producing antibiotics. In a previous study, we used deep sequencing to identify unprecedented frequencies of known resistance genes to several classes of antibiotics in these samples. In this study, we aim to functionally characterize the resistome in a more open and exploratory way by screening genomic DNA libraries transformed into sensitive hosts. To generate the libraries, several experimental strategies were explored, including mechanical shearing and enzymatic digestion of the isolated DNA followed by blunt- or sticky end cloning into different plasmids, subsequently transformed into sensitive E. coli. Pros and cons of the different strategies will be discussed along with preliminary results of the screening against selected antibiotics.
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| 57. |
- Alström, Per, et al.
(författare)
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Integrative taxonomy of the Russet Bush Warbler Locustella mandelli complex reveals a new species from central China
- 2015
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Ingår i: Avian Research. - : Elsevier BV. - 2053-7166. ; 6:9
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Russet Bush Warbler Locustella (previously Bradypterus) mandelli complex occurs in mountains in the eastern Himalayas, southern China, Vietnam, the Philippines, and Indonesia. The taxonomy has been debated, with one (L. seebohmi) to four (L. seebohmi, L. mandelli, L. montis and L. timorensis) species having been recognised. Methods: We used an integrative approach, incorporating analyses of morphology, vocalizations and a molecular marker, to re-evaluate species limits in the L. mandelli complex. Results: We found that central Chinese L. mandelli differed from those from India through northern Southeast Asia to southeast China in plumage, morphometrics and song. All were easily classified by song, and (wing + culmen)/tail ratio overlapped only marginally. Both groups were reciprocally monophyletic in a mitochondrial cytochrome b (cytb) gene tree, with a mean divergence of 1.0 +/- 0.2%. They were sympatric and mostly altitudinally segregated in the breeding season in southern Sichuan province. We found that the Mt Victoria (western Myanmar) population differed vocally from other L. mandelli, but no specimens are available. Taiwan Bush Warbler L. alishanensis was sister to the L. mandelli complex, with the most divergent song. Plumage, vocal and cytb evidence supported the distinctness of the south Vietnamese L. mandelli idonea. The Timor Bush Warbler L. timorensis, Javan Bush Warbler L. montis and Benguet Bush Warbler L. seebohmi differed distinctly in plumage, but among-population song variation in L. montis exceeded the differences between some populations of these taxa, and mean pairwise cytb divergences were only 0.5-0.9%. We also found that some L. montis populations differed morphologically. Conclusions: We conclude that the central Chinese population of Russet Bush Warbler represents a new species, which we describe herein, breeding at mid elevations in Sichuan, Shaanxi, Hubei, Hunan and Guizhou provinces. The taxonomic status of the other allopatric populations is less clear. However, as they differ to a degree comparable with that of the sympatric L. mandelli and the new species, we elevate L. idonea to species status, and retain L. seebohmi and L. montis as separate species, the latter with timorensis as a subspecies. Further research should focus on different populations of L. montis and the Mt Victoria population of L. mandelli.
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| 58. |
- Bates, Scott T., et al.
(författare)
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Meeting Report: Fungal ITS Workshop (October 2012)
- 2013
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Ingår i: Standards in Genomic Sciences. - : Springer Science and Business Media LLC. - 1944-3277. ; 8:1, s. 118-123
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Tidskriftsartikel (refereegranskat)abstract
- This report summarizes a meeting held in Boulder, CO USA (19–20 October 2012) on fungal community analyses using ultra-high-throughput sequencing of the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA (rRNA) genes. The meeting was organized as a two-day workshop, with the primary goal of supporting collaboration among researchers for improving fungal ITS sequence resources and developing recommendations for standard ITS primers for the research community.
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| 59. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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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
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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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| 60. |
- Dong, L., et al.
(författare)
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Taxonomy of the Narcissus Flycatcher Ficedula narcissina complex: an integrative approach using morphological, bioacoustic and multilocus DNA data
- 2015
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Ingår i: Ibis. - : Wiley. - 0019-1019 .- 1474-919X. ; 157:2, s. 312-325
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Tidskriftsartikel (refereegranskat)abstract
- The taxonomy of the Narcissus Flycatcher Ficedula narcissina-Yellow-rumped Flycatcher Ficedula zanthopygia complex from East Asia has long been debated. Most authors recognize two species: F.narcissina, with the subspecies narcissina (most of Japan and Sakhalin Island), owstoni (south Japanese islands) and elisae (northeast China) and F.zanthopygia (monotypic), although species status has been proposed for elisae and sometimes for owstoni. Here, we revise the taxonomy of this complex based on an integrative approach utilizing morphology, songs and mitochondrial and nuclear DNA for all taxa. All taxa were diagnosably different in plumage, and there were also structural differences among them, although the northernmost populations of owstoni (sometimes recognized as jakuschima and shonis) were somewhat intermediate in plumage, structure and male plumage maturation between southern populations of owstoni and narcissina. All taxa had different songs, and a discriminant function analysis of four song variables correctly classified 100% of all songs. A strongly supported phylogeny was recovered based on three mitochondrial genes and three nuclear introns (total of 3543bp), revealing a sister relationship between F.zanthopygia and the other taxa, between F.n.narcissina and F.n.owstoni, and between F.n.elisae and F.n.narcissina+F.n.owstoni. The corrected COI distances among the three F.narcissina subspecies ranged from 2.8% (narcissina-owstoni) to 8.2% (narcissina-elisae). We suggest that the congruent differences in multiple independent traits and the deep genetic divergences among the four taxa in the F.narcissina-F.zanthopygia complex support treatment of all of these taxa as separate species. However, we acknowledge the paucity of data for F.owstoni and recommend further studies of this taxon. We suggest listing both F.elisae and F.owstoni, which have small and fragmented populations, as globally threatened.
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