Molecular diversity assessment of arctic and boreal<i>Agaricus</i>taxa

Geml, József; Laursen, Gary A.; Taylor, D. Lee

doi:10.3852/07-042r1

Cited by 40 publications

(33 citation statements)

References 49 publications

(44 reference statements)

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“…OTUs similar to all the soil isolates examined for organic acid secretion and Pb solubilization in this study were also found in all samples in the pyrosequence analysis (at a Ն97% identity cutoff) (20,33). None of our isolates were dominant in these soils; however, they were present at levels greater than 1%, which is not necessarily uncommon for fungi (42,48).…”

Section: Discussionsupporting

confidence: 60%

Firing Range Soils Yield a Diverse Array of Fungal Isolates Capable of Organic Acid Production and Pb Mineral Solubilization

Sullivan

Gottel

Basta

et al. 2012

Appl Environ Microbiol

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e Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecularweight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil ؊1 . We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter ؊1 (18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as Aspergillus niger. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health.

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Section: Discussionsupporting

confidence: 60%

Firing Range Soils Yield a Diverse Array of Fungal Isolates Capable of Organic Acid Production and Pb Mineral Solubilization

Sullivan

Gottel

Basta

et al. 2012

Appl Environ Microbiol

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“…The resulting PCR libraries were shipped frozen to the Broad Institute, Cambridge Massachusettss (USA), where transformation, plating, colony picking, Templiphi reactions, and sequencing were carried out on automated equipment, using M13 forward and reverse vector primers. These molecular methods have been partially described elsewhere (Taylor et al 2007, Geml et al 2008. Site coordinates and numbers of soil cores and sequences generated are given in Appendix A: Tables A1 and A2.…”

Section: Pcr and Sequencingmentioning

confidence: 99%

A first comprehensive census of fungi in soil reveals both hyperdiversity and fine‐scale niche partitioning

Taylor

Hollingsworth

Mcfarland

et al. 2014

Ecological Monographs

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315

249

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Abstract. Fungi play key roles in ecosystems as mutualists, pathogens, and decomposers. Current estimates of global species richness are highly uncertain, and the importance of stochastic vs. deterministic forces in the assembly of fungal communities is unknown. Molecular studies have so far failed to reach saturated, comprehensive estimates of fungal diversity. To obtain a more accurate estimate of global fungal diversity, we used a direct molecular approach to census diversity in a boreal ecosystem with precisely known plant diversity, and we carefully evaluated adequacy of sampling and accuracy of species delineation. We achieved the first exhaustive enumeration of fungi in soil, recording 1002 taxa in this system. We show that the fungus : plant ratio in Picea mariana forest soils from interior Alaska is at least 17:1 and is regionally stable. A global extrapolation of this ratio would suggest 6 million species of fungi, as opposed to leading estimates ranging from 616 000 to 1.5 million. We also find that closely related fungi often occupy divergent niches. This pattern is seen in fungi spanning all major functional guilds and four phyla, suggesting a major role of deterministic niche partitioning in community assembly. Extinctions and range shifts are reorganizing biodiversity on Earth, yet our results suggest that 98% of fungi remain undescribed and that many of these species occupy unique niches.

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“…ITS is also used in some fungi for providing an indication of delimitation by a measure of the genetic distances (26). However, phylogenetic approaches are also being used to identify taxonomic units in environmental sampling of fungi (27) and are often more effective in comparison (28).…”

mentioning

confidence: 99%

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Schoch

Seifert

Huhndorf

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

4,242

2,910

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Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative proteincoding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter-and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.DNA barcoding | fungal biodiversity T he absence of a universally accepted DNA barcode for Fungi, the second most speciose eukaryotic kingdom (1, 2), is a serious limitation for multitaxon ecological and biodiversity studies. DNA barcoding uses standardized 500-to 800-bp sequences to identify species of all eukaryotic kingdoms using primers that are applicable for the broadest possible taxonomic group. Reference barcodes must be derived from expertly identified vouchers deposited in biological collections with online metadata and validated by available online sequence chromatograms. Interspecific variation should exceed intraspecific variation (the barcode gap), and barcoding is optimal when a sequence is constant and unique to one species (3, 4). Ideally, the barcode locus would be the same for all kingdoms. A region of the mitochondrial gene encoding the cytochrome c oxidase subunit 1 (CO1) is the barcode for animals (3, 4) and the default marker adopted by the Consortium for the Barcode of Life for all groups of organisms, including fungi (5). In Oomycota, part of the kingdom Stramenopila historically studied by mycologists, the de facto barcode internal transcribed spacer (ITS) region is suitable for identification, but the default CO1 marker is more reliable in a few clades of closely related species (6)...

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Molecular diversity assessment of arctic and borealAgaricustaxa

Cited by 40 publications

References 49 publications

Firing Range Soils Yield a Diverse Array of Fungal Isolates Capable of Organic Acid Production and Pb Mineral Solubilization

Firing Range Soils Yield a Diverse Array of Fungal Isolates Capable of Organic Acid Production and Pb Mineral Solubilization

A first comprehensive census of fungi in soil reveals both hyperdiversity and fine‐scale niche partitioning

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

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