A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning
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Jack W. McFarland | Niall J. Lennon | Chad Nusbaum | Teresa N. Hollingsworth | N. Lennon | C. Nusbaum | R. Ruess | D. Taylor | T. Hollingsworth | J. McFarland | Roger W. Ruess | D. Lee Taylor | D. Taylor
[1] E. Kristiansson,et al. A software pipeline for processing and identification of fungal ITS sequences , 2009, Source Code for Biology and Medicine.
[2] N. Lennon,et al. Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach , 2008, Molecular ecology resources.
[3] Andy F. S. Taylor,et al. Diversity and abundance of resupinate thelephoroid fungi as ectomycorrhizal symbionts in Swedish boreal forests , 2000, Molecular ecology.
[4] G. Mueller,et al. Assessment of tree species richness as a surrogate for macrofungal species richness , 2005 .
[5] Neil Brummitt,et al. Towards Target 1 of the Global Strategy for Plant Conservation : a working list of all known plant species-progress and prospects , 2008 .
[6] P. Legendre,et al. SPECIES ASSEMBLAGES AND INDICATOR SPECIES:THE NEED FOR A FLEXIBLE ASYMMETRICAL APPROACH , 1997 .
[7] G. B. Golding,et al. Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons? , 2011, The New phytologist.
[8] F. Martin,et al. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. , 2009, The New phytologist.
[9] J. Moncalvo,et al. Toward a better understanding of the infrageneric relationships in Cortinarius (Agaricales, Basidiomycota) , 2004, Mycologia.
[10] B. Horwitz,et al. Genomics of Soil- and Plant-Associated Fungi , 2013, Soil Biology.
[11] J. Geml,et al. Molecular diversity assessment of arctic and boreal Agaricus taxa , 2008, Mycologia.
[12] D. Bass,et al. Discovery of novel intermediate forms redefines the fungal tree of life , 2011, Nature.
[13] L. Olson,et al. Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling. , 2013, Molecular phylogenetics and evolution.
[14] T. E. Osterkamp,et al. The effect of permafrost thaw on old carbon release and net carbon exchange from tundra , 2009, Nature.
[15] P. Hammond,et al. Laboulbeniales on beetles: host utilization patterns and species richness of the parasites , 1997, Biodiversity & Conservation.
[16] T. James,et al. Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi , 2011, Science.
[17] Robert H. Whittaker,et al. Vegetation of the Santa Catalina Mountains, Arizona: A Gradient Analysis of the South Slope , 1965 .
[18] T. Horton. Molecular approaches to ectomycorrhizal diversity studies: variation in ITS at a local scale , 2002, Plant and Soil.
[19] Robert M. May,et al. How Many Species Are There on Earth? , 1988, Science.
[20] C. Kubicek,et al. Phylogeny of the genus trichoderma based on sequence analysis of the internal transcribed spacer region 1 of the rDNA cluster , 1998, Fungal genetics and biology : FG & B.
[21] S. Trumbore,et al. Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. , 2007, The New phytologist.
[22] V. Kunin,et al. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. , 2009, Environmental microbiology.
[23] J. Bever. Feeback between Plants and Their Soil Communities in an Old Field Community , 1994 .
[24] J. Losos. Chapter 14. Historical Contingency and Lizard Community Ecology , 1994 .
[25] F. Chapin,et al. Plant Community Composition as a Predictor of Regional Soil Carbon Storage in Alaskan Boreal Black Spruce Ecosystems , 2008, Ecosystems.
[26] Campbell O. Webb,et al. Phylogenies and Community Ecology , 2002 .
[27] T. L. Esslinger,et al. A sixth checklist of the lichen-forming, lichenicolous, and allied fungi of the continental United States and Canada , 1987 .
[28] T. Henkel,et al. Towards global patterns in the diversity and community structure of ectomycorrhizal fungi. , 2012, Molecular ecology.
[29] J. Rougemont,et al. A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.
[30] Vladimir E. Romanovsky,et al. Evidence for warming and thawing of discontinuous permafrost in Alaska , 1999 .
[31] D. Tilman. Resource competition and community structure. , 1983, Monographs in population biology.
[32] F. Chapin,et al. Scale-dependent environmental controls over species composition in Alaskan black spruce communities , 2006 .
[33] M. McCormick,et al. Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas. , 2008, The New phytologist.
[34] G. Gilbert,et al. Host Specialization among Wood-Decay Polypore Fungi in a Caribbean Mangrove Forest1 , 2002 .
[35] C. Stern. CONCLUDING REMARKS OF THE CHAIRMAN , 1950 .
[36] R. May. A fondness for fungi , 1991, Nature.
[37] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[38] Andy F. S. Taylor,et al. Species composition of an ectomycorrhizal fungal community along a local nutrient gradient in a boreal forest. , 2006, The New phytologist.
[39] T. White,et al. Identification of indigenous and introduced symbiotic fungi in ectomycorrhizae by amplification of nuclear and mitochondrial ribosomal DNA , 1991 .
[40] H. Ashton. Ainsworth and Bisby's Dictionary of the Fungi (10th edition) , 2009 .
[41] T. Bruns,et al. Community structure of ectomycorrhizal fungi in a Pinus muricata forest: above- and below-ground views , 1996 .
[42] I. Longden,et al. EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.
[43] H. Nusbaum,et al. Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria) , 2005, Molecular ecology.
[44] N. Lennon,et al. 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 .
[45] W. Silver,et al. Interactions between Aboveground and Belowground Biodiversity in Terrestrial Ecosystems: Patterns, Mechanisms, and Feedbacks , 2000 .
[46] S. Hubbell,et al. The unified neutral theory of biodiversity and biogeography at age ten. , 2011, Trends in ecology & evolution.
[47] B. McCune,et al. Analysis of Ecological Communities , 2002 .
[48] M. A. Leibold. The Niche Concept Revisited: Mechanistic Models and Community Context , 1995 .
[49] M. Blackwell,et al. Taxonomic diversity and interactions of insect-associated ascomycetes , 1997, Biodiversity & Conservation.
[50] Rytas Vilgalys,et al. Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples , 2005, Applied and Environmental Microbiology.
[51] Alisa L. Gallant,et al. Ecoregions of Alaska , 1995 .
[52] K. Kvamme,et al. Improvements in the Permutation Test for the Spatial Analysis of the Distribution of Artifacts into Classes , 1983, American Antiquity.
[53] D. Hawksworth,et al. Where are all the undescribed fungi? , 1997, Phytopathology.
[54] C. Mora,et al. How Many Species Are There on Earth and in the Ocean? , 2011, PLoS biology.
[55] R. Humber. Synopsis of a revised classification for the Entomophthorales (Zygomycotina) , 1989 .
[56] N. Lennon,et al. Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula (Russulales; Basidiomycota). , 2010, The New phytologist.
[57] R. Halvorsen,et al. Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing. , 2012, The New phytologist.
[58] C. Marshall,et al. Has the Earth’s sixth mass extinction already arrived? , 2011, Nature.
[59] R. Ruess,et al. Contributions of fine root production and turnover to the carbon and nitrogen cycling in taiga forests of the Alaskan interior , 1996 .
[60] D. Pollock,et al. The beetle gut: a hyperdiverse source of novel yeasts. , 2005, Mycological research.
[61] D. Rizzo,et al. Ectomycorrhizal community structure in a xeric Quercus woodland based on rDNA sequence analysis of sporocarps and pooled roots. , 2007, The New phytologist.
[62] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[63] D. Hopkins,et al. Quaternary Geology and Archaeology of Alaska , 1965 .
[64] D. L. Hawksworth. Global species numbers of fungi: are tropical studies and molecular approaches contributing to a more robust estimate? , 2012, Biodiversity and Conservation.
[65] C. Quince,et al. Accurate determination of microbial diversity from 454 pyrosequencing data , 2009, Nature Methods.
[66] Jonathan Silvertown,et al. Plant coexistence and the niche , 2004 .
[67] J. G. Skellam. Random dispersal in theoretical populations , 1951, Biometrika.
[68] P. Sale. Maintenance of High Diversity in Coral Reef Fish Communities , 1977, The American Naturalist.
[69] D. Taylor,et al. A bioinformatics pipeline for sequence-based analyses of fungal biodiversity. , 2011, Methods in molecular biology.
[70] Rob Knight,et al. UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..
[71] T. White. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics , 1990 .
[72] Eric S. Kasischke,et al. Resilience of Alaska's Boreal Forest to Climatic Change , 2010 .
[73] Erik Kristiansson,et al. Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota) , 2008, BMC Evolutionary Biology.
[74] Thomas Ludwig,et al. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees , 2005, Bioinform..
[75] C. T. Dyrness,et al. Introduction and overview of a multidisciplinary research project: the structure and function of a black spruce (Piceamariana) forest in relation to other fire-affected taiga ecosystems , 1983 .
[76] N. Lennon,et al. Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA , 2009, Molecular ecology.
[77] John L. Spouge,et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi , 2012, Proceedings of the National Academy of Sciences.
[78] D. Taylor,et al. Structure and resilience of fungal communities in Alaskan boreal forest soils , 2010 .
[79] X. Huang,et al. CAP3: A DNA sequence assembly program. , 1999, Genome research.
[80] J. Kruskal. Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis , 1964 .
[81] J. Grinnell. The Niche-Relationships of the California Thrasher , 1917 .
[82] P. Green,et al. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.
[83] Aaron M.Ellison. PC‐ORD: Multivariate Analysis of Ecological Data , 1998, The Bulletin of the Ecological Society of America.
[84] E. Willerslev,et al. Review Paper. Ancient DNA , 2005, Proceedings of the Royal Society B: Biological Sciences.
[85] G. F. Gause. Experimental Studies on the Struggle for Existence: I. Mixed Population of Two Species of Yeast , 1932 .
[86] K. Jones,et al. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. , 2009, The New phytologist.
[87] James Long,et al. TOPO TA is A-OK: a test of phylogenetic bias in fungal environmental clone library construction. , 2007, Environmental microbiology.
[88] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[89] F. Lutzoni,et al. Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? , 2007, Ecology.
[90] Samuel Rieger,et al. Soil Survey: Fairbanks Area, Alaska , 1963 .
[91] R. Koide,et al. Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. , 2002, The New phytologist.
[92] J. Ammirati,et al. Species richness and abundance of ectomycorrhizal basidiomycete sporocarps on a moisture gradient in the Tsuga heterophylla zone , 1999 .
[93] R. Macarthur,et al. The Limiting Similarity, Convergence, and Divergence of Coexisting Species , 1967, The American Naturalist.
[94] R. Henrik Nilsson,et al. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences , 2011 .
[95] David L. Hawksworth,et al. The fungal dimension of biodiversity: magnitude, significance, and conservation , 1991 .
[96] D. Taylor,et al. Peeking through a frosty window: molecular insights into the ecology of Arctic soil fungi. , 2012 .
[97] Relationships between soil microbial diversity and plant community structure in seminatural grasslands , 2008 .
[98] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[99] M. Mayfield,et al. Opposing effects of competitive exclusion on the phylogenetic structure of communities. , 2010, Ecology letters.