FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

Fungal Ecology - Tập 20 - Trang 241-248 - 2016
Nhu H. Nguyen1, Zewei Song2, Scott T. Bates2, Sara Branco3, Leho Tedersoo4, Jon Menke1, Jonathan S. Schilling5, Peter G. Kennedy1,6
1Department of Plant Biology, University of Minnesota, St. Paul, MN USA
2Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
3Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
4Natural History Museum, University of Tartu, Tartu, Estonia
5Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, USA
6Department of Ecology, Evolution, & Behavior, University of Minnesota, St. Paul, MN, USA

Tài liệu tham khảo

Abarenkov, 2010, The UNITE database for molecular identification of fungi–recent updates and future perspectives, New. Phytol., 186, 281, 10.1111/j.1469-8137.2009.03160.x Abarenkov, 2010, PlutoF—a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences, Evol. Bioinform., 6, 189, 10.4137/EBO.S6271 Agerer, 2001, Exploration types of ectomycorrhizae: a proposal to classify ectomycorrhizal mycelial systems according to their patterns of differentiation and putative ecological importance, Mycorrhiza, 11, 107, 10.1007/s005720100108 Alexopoulos, 1996 Amend, 2010, Quantifying microbial communities with 454 pyrosequencing: does read abundance count?, Mol. Ecol., 19, 5555, 10.1111/j.1365-294X.2010.04898.x Baldrian, 2012, Active and total microbial communities in forest soil are largely different and highly stratified during decomposition, ISME J., 6, 248, 10.1038/ismej.2011.95 Bates, 2013, Global biogeography of highly diverse protistan communities in soil, ISME J., 7, 652, 10.1038/ismej.2012.147 Bidartondo, 2008, Preserving accuracy in GenBank, Science, 319, 5870, 10.1126/science.319.5870.1616a Blackwell, 2011, The Fungi: 1, 2, 3… 5.1 million species?, Am. J. Bot., 98, 426, 10.3732/ajb.1000298 Branco, 2013, Fungi at a small scale: spatial zonation of fungal assemblages around single trees, PLoS One, 8, e78295, 10.1371/journal.pone.0078295 Brundrett, 2009, Mycorrhizal associations and other means of nutrition of vascular plants: understanding the global diversity of host plants by resolving conflicting information and developing reliable means of diagnosis, Plant Soil, 230, 37, 10.1007/s11104-008-9877-9 Buée, 2009, 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity, New. Phytol., 184, 449, 10.1111/j.1469-8137.2009.03003.x Burdsall, 1985 Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335, 10.1038/nmeth.f.303 Caporaso, 2011, Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proc. Natl. Acad. Sci., 108, 4516, 10.1073/pnas.1000080107 Clemmensen, 2013, Roots and associated fungi drive long-term carbon sequestration in boreal forest, Science, 339, 1615, 10.1126/science.1231923 Clemmensen, 2015, Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests, New. Phytol., 205, 1525, 10.1111/nph.13208 Cummins, 2003 Dighton, 2003 Filiatrault, 2011, Progress in prokaryotic transcriptomics, Curr. Opin. Microbiol., 14, 579, 10.1016/j.mib.2011.07.023 Gadgil, 1971, Mycorrhiza and litter decomposition, Nature, 233, 133, 10.1038/233133a0 Gotelli, 2004, A taxonomic wish-list for community ecology, Philos. Trans. R. Soc. Lond. B. Biol. Sci., 585, 10.1098/rstb.2003.1443 Hawkins, 1989, Guilds: the multiple meanings of a concept, Annu. Rev. Entomol., 34, 423, 10.1146/annurev.en.34.010189.002231 Herr, 2014, Towards the unification of microorganisms, New. Phytol., 205, 27, 10.1111/nph.13180 Hibbett, 2013, Toward genome-enabled mycology, Mycologia, 105, 1339, 10.3852/13-196 Högberg, 2003, Contrasting effects of nitrogen availability on plant carbon supply to mycorrhizal fungi and saprotrophs – a hypothesis based on field observations in boreal forest, New. Phytol., 160, 225, 10.1046/j.1469-8137.2003.00867.x Kerekes, 2013, Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest, Mol. Ecol., 22, 2827, 10.1111/mec.12259 Koele, 2014, Ecological significance of mineral weathering in ectomycorrhizal and arbuscular mycorrhizal ecosystems from a field-based comparison, Soil Biol. Biochem., 69, 63, 10.1016/j.soilbio.2013.10.041 Kõljalg, 2013, Towards a unified paradigm for sequence-based identification of fungi, Mol. Ecol., 22, 5271, 10.1111/mec.12481 Kubartová, 2012, Patterns of fungal communities among and within decaying logs, revealed by 454 sequencing, Mol. Ecol., 21, 4514, 10.1111/j.1365-294X.2012.05723.x Kuo, 2014, Secret lifestyles of Neurospora crassa, Sci. Rep., 4, 5135, 10.1038/srep05135 Lambert, 1981, Biogeography of the Colorado herpetofauna, Am. Midl. Nat., 106, 145, 10.2307/2425144 Langille, 2013, Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nat. Biotechnol., 31, 814, 10.1038/nbt.2676 Lekberg, 2014, Will different OTU delineation methods change interpretation of arbuscular mycorrhizal fungal community patterns?, New. Phytol., 202, 1101, 10.1111/nph.12758 Lindahl, 1999, Translocation of 32P between interacting mycelia of a wood-decomposing fungus and ectomycorrhizal fungi in microcosm systems, New. Phytol., 144, 183, 10.1046/j.1469-8137.1999.00502.x Münzenberger, 2012, Morphology, anatomy, and molecular studies of the ectomycorrhiza formed axenically by the fungus Sistotrema sp. (Basidiomycota), Mycol. Prog., 11, 817, 10.1007/s11557-011-0797-3 Nguyen, 2015, Parsing ecological signal from noise in next generation amplicon sequencing, New. Phytol., 205, 1389, 10.1111/nph.12923 Nilsson, 2008, Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species Identification, Evol. Bioinform., 4, 193, 10.4137/EBO.S653 Nilsson, 2006, Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective, PLoS One, 1, e59, 10.1371/journal.pone.0000059 Ottosson, 2014, Species associations during the succession of wood-inhabiting fungal communities, Fungal Ecol., 11, 17, 10.1016/j.funeco.2014.03.003 Parfitt, 2010, Do all trees carry the seeds of their own destruction? PCR reveals numerous wood decay fungi latently present in sapwood of a wide range of angiosperm trees, Fungal Ecol., 3, 338, 10.1016/j.funeco.2010.02.001 Peay, 2014, Back to the future: natural history and the way forward in modern fungal ecology, Fungal Ecol., 2, 4, 10.1016/j.funeco.2014.06.001 Peay, 2013, Strong coupling of plant and fungal community structure across western Amazonian rainforests, ISME J., 7, 1852, 10.1038/ismej.2013.66 Peay, 2012, Measuring ectomycorrhizal fungal dispersal: macroecological patterns driven by microscopic propagules, Mol. Ecol., 21, 4122, 10.1111/j.1365-294X.2012.05666.x Prober, 2015, Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide, Ecol. Lett., 18, 85, 10.1111/ele.12381 Promputtha, 2007, A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence, Microb. Ecol., 53, 579, 10.1007/s00248-006-9117-x Riley, 2014, Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi, Proc. Natl. Acad. Sci., 111, 10.1073/pnas.1400592111 Root, 1967, The niche exploitation pattern of the blue-gray gnatcatcher, Ecol. Monogr., 37, 317, 10.2307/1942327 Rosling, 2011, Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi, Science, 333, 876, 10.1126/science.1206958 Schadt, 2003, Seasonal dynamics of previously unknown fungal lineages in tundra soils, Science, 301, 1359, 10.1126/science.1086940 Schilling, 2015, Signature wood modifications reveal decomposer community history, PLOS One, 10, e0120679, 10.1371/journal.pone.0120679 Schimper, 1902 Shokralla, 2012, Next-generation sequencing technologies for environmental DNA research, Mol. Ecol., 21, 1794, 10.1111/j.1365-294X.2012.05538.x Sieber, 2007, Endophytic fungi in forest trees: are they mutualists?, Fungal Biol. Rev., 21, 75, 10.1016/j.fbr.2007.05.004 Simberloff, 1991, The guild concept and the structure of ecological communities, Annu. Rev. Ecol. Syst., 22, 115, 10.1146/annurev.es.22.110191.000555 Smith, 2014, Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing, PLoS One, 9, e90234, 10.1371/journal.pone.0090234 Štursová, 2014, When the forest dies: the response of forest soil fungi to a bark beetle-induced tree dieback, ISME J., 8, 1920, 10.1038/ismej.2014.37 Talbot, 2014, Endemism and functional convergence across the North American soil mycobiome, Proc. Natl. Acad. Sci. U. S. A., 111, 6341, 10.1073/pnas.1402584111 Taylor, 2014, A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning, Ecol. Monogr., 84, 3, 10.1890/12-1693.1 Tedersoo, 2015, Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi, MycoKeys, 10, 1, 10.3897/mycokeys.10.4852 Tedersoo, 2014, Global diversity and geography of soil fungi, Science, 80 Tedersoo, 2013, Lineages of ectomycorrhizal fungi revisited: foraging strategies and novel lineages revealed by sequences from belowground, Fungal Biol. Rev., 27, 83, 10.1016/j.fbr.2013.09.001 Terborgh, 1986, Guilds and their utility in ecology, 65 Tewksbury, 2014, Natural history's place in science and society, Biosci., 64, 300, 10.1093/biosci/biu032 Walter, 1989, Species, guilds, and functional groups: taxonomy and behavior in nematophagous arthropods, J. Nematol., 21, 315 Wang, 2007, Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol., 73, 5261, 10.1128/AEM.00062-07 Wilson, 1999, Guilds, functional types and ecological groups, Oikos, 86, 507, 10.2307/3546655 Worrall, 1997, Comparison of wood decay among diverse lignicolous fungi, Mycologia, 89, 199, 10.1080/00275514.1997.12026772