Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples

By Heath E. O’Brien, J. Parrent, J. A. Jackson, Jean-Marc Moncalvo, R. Vilgalys. Applied and Environmental Microbiology, 2005

972 citations recorded by the source corpus.

Subfields: Cell Biology, Ecology, Evolution, Behavior and Systematics, Plant Science

View Paper: https://www.semanticscholar.org/paper/bc5c20bcd08c6354a92133495a85ce0124e4d97d

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Citations in the corpus

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. (2009, methodology): “In a second analysis, the individual sample FASTA files were evaluated using NCBI-BLASTn (Altschul et al., 1997) against the nonredundant GenBank database (Benson et al., 2008) and C-DB derived from the GenBank and UNITE (Kõljalg et al., 2005; http://unite.ut.ee/index.php) databases.”
The endophytic mycota associated with Vitis vinifera in central Spain (2011, neutral): “…both intra-genus or intraspecies level depending on the type of fungal group analysed, arbitrary thresholds similar to those used in the present study have been previously used in other endophyte-related studies to identify taxa (O’Brien et al. 2005; Neubert et al. 2006; Sánchez et al. 2007, 2008).”
Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. (2007, background): “Journal compilation © New Phytologist (2006) doi : 10.1111/j.1469-8137.2006.01936.x Author for correspondence: Björn Lindahl Tel: +46 18 672725 Fax: +46 18 673599 Email: bjorn.lindahl@mykopat.slu.se Received: 30 August 2006 Accepted: 22 September 2006”
“Missing” protists: a molecular prospective (2008, background): “In fact, molecular surveys targeting speciWcally fungal communities show that fungi are extremely diverse in soils, and particularly forest soils (Anderson and Cairney 2004; O’Brien et al. 2005).”
An arctic community of symbiotic fungi assembled by long‐distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA (2012, methodology): “Although there is no universal cut-off value for species delimitation in fungi, we used 97% ITS sequence similarity based on previous studies (e.g. O’Brien et al., 2005; Arnold & Lutzoni, 2007; Higgins et al., 2007; Geml et al., 2009), because this cut-off value tends to provide a conservative, yet…”
Three reasons to re-evaluate fungal diversity 'on Earth and in the ocean' (2011, methodology): “1 M OTUs (O’brien et al., 2005).”
Production of extracellular enzymes and degradation of biopolymers by saprotrophic microfungi from the upper layers of forest soil (2010, background): “oxidation and humic acid bleaching were negative and because the presence of these enzymes is not anticipated in nonbasidiomycetous fungi ( Morgenstern et al. 2008 ).”
Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences (2011, background): “…g io n C lu st e ri n g th ro u g h it e ra te d B L A S T se a rc h e s a t 9 8 .5 % (2001), or at least forty-four to one, based on the diversity estimates of O’Brien et al. (2005) (these odds are also based on an admittedly na€ıve assumption that all species are uniformly distributed in nature).”
Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays (2005, background): “The high relative abundance of basidiomycete fungi in the forest soil (Fig. 2) has been observed in fungal clone libraries constructed from soil collected at the site ( 19 ).”
Microbial activity and soil respiration under nitrogen addition in Alaskan boreal forest (2008, background): “Using molecular surveys, O’Brien et al. (2005) also found that Agaricales dominated the Basidiomycete communities of surface soils in a forested ecosystem.”
Microbial Biogeography: Patterns in Microbial Diversity across Space and Time (2008, positive): “Recent evidence suggests that bacteria are not unique in this regard as other microbial groups (including protists,viruses, archaea, and fungi) may also exhibit very high levels of local phylogenetic diversity (Breitbart et al., 2002; Fierer et al., In Press; O'Brien et al., 2005; Walsh et al., 2005”
Fungal Diversity Revisited: 2.2 to 3.8 Million Species (2017, background): “…rates of new taxa (2), plant:fungus ratios (3, 4) similar to plant:insect ratios ﬁ rst used in Erwin ’ s famous study (5), quantitative macroecological grid-based approaches (6 – 8), methods based on environmental sequence data including plant:fungus ratios (9, 10), and ecological scaling laws (1).”