UNITE: a database providing web‐based methods for the molecular identification of ectomycorrhizal fungi

Kõljalg, Urmas; Larsson, Karl‐Henrik; Abarenkov, Kessy; Nilsson, R. Henrik; Alexander, Ian J.; Eberhardt, Ursula; Erland, Susanne; Høiland, Klaus; Kjøller, Rasmus; Larsson, Ellen; Pennanen, Taina; Sen, Robin; Taylor, Andy F. S.; Tedersoo, Leho; Vrålstad, Trude; Ursing, Björn M.

doi:10.1111/j.1469-8137.2005.01376.x

Cited by 929 publications

(632 citation statements)

References 31 publications

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“…Forward and reverse DNA sequences of the ITS1 region were edited and aligned using Bioedit v7.1.11 (Hall 1999) and compared with all fungal sequences available through the BLAST Network Service (National Center for Biotechnology Service, NCBI; http://www.ncbi.nlm.nih.gov/ BLAST) and the UNITE database (Kõljalg et al 2005) using the BLASTn algorithm (Altschul et al 1997). All generated DNA sequence data have been deposited with the EMBL/GenBank Data Libraries and are available under accession nos.…”

Section: Resultsmentioning

confidence: 99%

Large and variable genome size unrelated to serpentine adaptation but supportive of cryptic sexuality in Cenococcum geophilum

et al. 2013

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Estimations of genome size and its variation can provide valuable information regarding the genetic diversity of organisms and their adaptation potential to heterogeneous environments. We used flow cytometry to characterize the variation in genome size among 40 isolates of Cenococcum geophilum, an ectomycorrhizal fungus with a wide ecological and geographical distribution, obtained from two serpentine and two non-serpentine sites in Portugal. Besides determining the genome size and its intraspecies variation, we wanted to assess whether a relationship exists between genome size and the edaphic background of the C. geophilum isolates. Our results reveal C. geophilum to have one of the largest genome sizes so far measured in the Ascomycota, with a mean haploid genome size estimate of 0.208 pg (203 Mbp). However, no relationship was found between genome size and the edaphic background of the sampled isolates, indicating genetic and demographic processes to be more important for shaping the genome size variation in this species than environmental selection. The detection of variation in ploidy level among our isolates, including a single individual with both presumed haploid and diploid nuclei, provides supportive evidence for a possible cryptic sexual or parasexual cycle in C. geophilum (although other mechanisms may have caused this variation). The existence of such a cycle would have wide significance, explaining the high levels of genetic diversity and likelihood of recombination previously reported in this species, and adds to the increasing number of studies suggesting sexual cycles in previously assumed asexual fungi.

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Section: Resultsmentioning

confidence: 99%

Large and variable genome size unrelated to serpentine adaptation but supportive of cryptic sexuality in Cenococcum geophilum

et al. 2013

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“…Database at both GenBank (Benson et al, 2005) and the UNITE (Kõljalg et al, 2005) (updated August 2014.) were used to determine the identity of sequences.…”

Section: Effect Of Temperature Ph Carbon and Nitrogen Sources On Mymentioning

confidence: 99%

Effects of temperature, pH and carbon and nitrogen sources on growth of in vitro cultures of ectomycorrhizal isolates from Pinus heldreichii forest

2016

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Aim of study: This study aims to provide basic information about physiological characteristics of isolates of Lactarius deliciosus (L.) Gray, Russula sanguinaria (Schumach.) Rauschert, Suillus collinitus (Fr) Kuntze, Suillus granulatus (L.) Rousell, Tricholoma batchii Gulden and Tricholoma imbricatum (Fr.) Kumm.Area of study: The isolates are obtained from Pinus heldreichii H. Christ forest in the south-eastern part of Montenegro. Material and methods:The isolates were molecularly characterised by internal transcribed spacer (ITS) sequencing and restriction fragment length polymorphism (RFLP) analysis. The effects of different temperatures (20, 22, 25°C), pHs (4, 4.5, 5.2, 5.8, 6.5, 7.5), and carbon (glucose, sucrose, dextrin, arabinose, xylose and starch) and nitrogen (NH 4 + , NO 3 -and protein) sources on their growth were examined under laboratory conditions.Main results: The studied factors established significant differences in the development of isolates. Isolates of R. sanguinaria, L. deliciosus and both Suillus, were characterised by faster growth at 22°C, while Tricholoma isolates grew faster at 25°C. S. granulatus, S. collinitus and T. imbticatum isolates grew well at lower pH values (4 -5.2), while L. deliciosus, R. sanguinaria and T. bachii exhibited faster growth at pHs between 5.8 and 6.5. The examined isolates were able to utilize various carbohydrates as carbon sources. The biggest mycelial growth was characterised for sucrose, then glucose, dextrin, arabinose, starch and xylose. They grew on all examined nitrogen sources, while the biggest mycelia growth was achieved on ammonium, followed by nitrate and protein. Those characteristics varied amongst the species.Research highlights: Information about physiological characteristics of Tricholoma, Lactarius, Russula, as well as Suillus, are sparse. Hence, the data obtained in this study could contribute to the understanding of their function in ecosystems.Keywords: Lactarius; Montenegro; physiology; RFLP analysis; Russula; Suillus; Tricholoma. Citation: Lazarević, J., Stojičić, D., Keča, N. (2016). Effects of temperature, pH and carbon and nitrogen sources on growth of in vitro cultures of ectomycorrrhizal isolates from Pinus heldreichii forest. Forest Systems, Volume 25, Issue 1, e048. http://dx.doi.

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“…Demultiplexed reads were used to construct a de novo database by removing sequences with an expected error rate of <0.5-bp per sequence, dereplicating them, removing unique sequences (i.e., singletons), and clustering the remaining sequences into operational taxonomic units (OTUs) at the 97 % similarity threshold. An additional quality control measure was taken by removing sequences from this dataset <75 % similar to any sequence in the UNITE database [54,55]. Raw demultiplexed sequences were then mapped to this filtered database at the 97 % similarity threshold to calculate sequence counts per OTU per sample.…”

Section: Fungal Sequencingmentioning

confidence: 99%

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

et al. 2014

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Human land use alters soil microbial composition and function in a variety of systems, although few comparable studies have been done in tropical forests and tropical agricultural production areas. Logging and the expansion of oil palm agriculture are two of the most significant drivers of tropical deforestation, and the latter is most prevalent in Southeast Asia. The aim of this study was to compare soil fungal communities from three sites in Malaysia that represent three of the most dominant land-use types in the Southeast Asia tropics: a primary forest, a regenerating forest that had been selectively logged 50 years previously, and a 25-year-old oil palm plantation. Soil cores were collected from three replicate plots at each site, and fungal communities were sequenced using the Illumina platform. Extracellular enzyme assays were assessed as a proxy for soil microbial function. We found that fungal communities were distinct across all sites, although fungal composition in the regenerating forest was more similar to the primary forest than either forest community was to the oil palm site. Ectomycorrhizal fungi, which are important associates of the dominant Dipterocarpaceae tree family in this region, were compositionally distinct across forests, but were nearly absent from oil palm soils. Extracellular enzyme assays indicated that the soil ecosystem in oil palm plantations experienced altered nutrient cycling dynamics, but there were few differences between regenerating and primary forest soils. Together, these results show that logging and the replacement of primary forest with oil palm plantations alter fungal community and function, although forests regenerating from logging had more similarities with primary forests in terms of fungal composition and nutrient cycling potential. Since oil palm agriculture is currently the mostly rapidly expanding equatorial crop and logging is pervasive across tropical ecosystems, these findings may have broad applicability.

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UNITE: a database providing web‐based methods for the molecular identification of ectomycorrhizal fungi

Cited by 929 publications

References 31 publications

Large and variable genome size unrelated to serpentine adaptation but supportive of cryptic sexuality in Cenococcum geophilum

Large and variable genome size unrelated to serpentine adaptation but supportive of cryptic sexuality in Cenococcum geophilum

Effects of temperature, pH and carbon and nitrogen sources on growth of in vitro cultures of ectomycorrhizal isolates from Pinus heldreichii forest

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

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