The DOI matches its Crossref record; 108 of the 108 references it cites were found in a registry or an index.
Fungal community analysis by high‐throughput sequencing of amplified markers – a user's guide
Open accessAbstract
Summary: Novel high‐throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant‐associated endophytes, pathogens, and mycorrhizal symbionts, as well as free‐living saprotrophs. Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large‐scale sequencing projects risk yielding artificial results and misleading conclusions.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics
White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990) · PCR Protocols · doi:10.1016/b978-0-12-372180-8.50042-1 · Cited by 36,648
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,826
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,885
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 19,549
PCR protocols — A guide to methods and applications
U.G. (1990) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(90)90252-7 · Cited by 11,702
GARDES, M., & BRUNS, T. D. (1993) · Molecular Ecology · doi:10.1111/j.1365-294x.1993.tb00005.x · Cited by 10,480
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glockner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,668
Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., Levesque, C. A., Chen, W., Fungal Barcoding Consortium, Fungal Barcoding Consortium Author List, Bolchacova, E., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1117018109 · Cited by 5,120
Self-citationChimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., Sodergren, E., et al. (2011) · Genome Research · doi:10.1101/gr.112730.110 · Cited by 3,473
Inhibition and facilitation of nucleic acid amplification
Wilson, I. G. (1997) · Applied and Environmental Microbiology · doi:10.1128/aem.63.10.3741-3751.1997 · Cited by 2,266
Ihrmark, K., Bödeker, I. T. M., Cruz-Martinez, K., Friberg, H., Kubartova, A., Schenck, J., Strid, Y., Stenlid, J., Brandström-Durling, M., Clemmensen, K. E., et al. (2012) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2012.01437.x · Cited by 2,098
Self-citationThe UNITE database for molecular identification of fungi – recent updates and future perspectives
Abarenkov, K., Henrik Nilsson, R., Larsson, K., Alexander, I. J., Eberhardt, U., Erland, S., Høiland, K., Kjøller, R., Larsson, E., Pennanen, T., et al. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2009.03160.x · Cited by 1,927
Self-citationReconstructing the early evolution of Fungi using a six-gene phylogeny
James, T. Y., Kauff, F., Schoch, C. L., Matheny, P. B., Hofstetter, V., Cox, C. J., Celio, G., Gueidan, C., Fraker, E., Miadlikowska, J., et al. (2006) · Nature · doi:10.1038/nature05110 · Cited by 1,815
Removing Noise From Pyrosequenced Amplicons
Quince, C., Lanzen, A., Davenport, R. J., & Turnbaugh, P. J. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-38 · Cited by 1,592
Integrative analysis of environmental sequences using MEGAN4
Huson, D. H., Mitra, S., Ruscheweyh, H.-J., Weber, N., & Schuster, S. C. (2011) · Genome Research · doi:10.1101/gr.120618.111 · Cited by 1,541
Bias in template-to-product ratios in multitemplate PCR
Polz, M. F., & Cavanaugh, C. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.10.3724-3730.1998 · Cited by 1,484
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346
Kunin, V., Engelbrektson, A., Ochman, H., & Hugenholtz, P. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02051.x · Cited by 1,277
Toju, H., Tanabe, A. S., Yamamoto, S., & Sato, H. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040863 · Cited by 1,256
Öpik, M., Vanatoa, A., Vanatoa, E., Moora, M., Davison, J., Kalwij, J. M., Reier, Ü., & Zobel, M. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03334.x · Cited by 1,178
ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases
Bellemain, E., Carlsen, T., Brochmann, C., Coissac, E., Taberlet, P., & Kauserud, H. (2010) · BMC Microbiology · doi:10.1186/1471-2180-10-189 · Cited by 1,148
Self-citationHamady, M., Lozupone, C., & Knight, R. (2010) · The ISME Journal · doi:10.1038/ismej.2009.97 · Cited by 1,099
Tedersoo, L., May, T. W., & Smith, M. E. (2010) · Mycorrhiza · doi:10.1007/s00572-009-0274-x · Cited by 1,016
Self-citation454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity
Buée, M., Reich, M., Murat, C., Morin, E., Nilsson, R. H., Uroz, S., & Martin, F. (2009) · New Phytologist · doi:10.1111/j.1469-8137.2009.03003.x · Cited by 1,006
Self-citationAccurate determination of microbial diversity from 454 pyrosequencing data
Quince, C., Lanzén, A., Curtis, T. P., Davenport, R. J., Hall, N., Head, I. M., Read, L. F., & Sloan, W. T. (2009) · Nature Methods · doi:10.1038/nmeth.1361 · Cited by 1,000
Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest
Lindahl, B. D., Ihrmark, K., Boberg, J., Trumbore, S. E., Högberg, P., Stenlid, J., & Finlay, R. D. (2007) · New Phytologist · doi:10.1111/j.1469-8137.2006.01936.x · Cited by 965
Self-citationField guide to next‐generation DNA sequencers
GLENN, T. C. (2011) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2011.03024.x · Cited by 940
Next‐generation sequencing technologies for environmental DNA research
SHOKRALLA, S., SPALL, J. L., GIBSON, J. F., & HAJIBABAEI, M. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05538.x · Cited by 925
Nilsson, R. H., Kristiansson, E., Ryberg, M., Hallenberg, N., & Larsson, K.-H. (2008) · Evolutionary Bioinformatics · doi:10.4137/ebo.s653 · Cited by 875
Self-citationLee, J., Lee, S., & Young, J. P. W. (2008) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2008.00531.x · Cited by 871
Baldrian, P., Kolařík, M., Štursová, M., Kopecký, J., Valášková, V., Větrovský, T., Žifčáková, L., Šnajdr, J., Rídl, J., Vlček, Č., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2011.95 · Cited by 860
DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods
Martin-Laurent, F., Philippot, L., Hallet, S., Chaussod, R., Germon, J. C., Soulas, G., & Catroux, G. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.5.2354-2359.2001 · Cited by 727
The fungus Armillaria bulbosa is among the largest and oldest living organisms
Smith, M. L., Bruhn, J. N., & Anderson, J. B. (1992) · Nature · doi:10.1038/356428a0 · Cited by 698
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
Reeder, J., & Knight, R. (2010) · Nature Methods · doi:10.1038/nmeth0910-668b · Cited by 678
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
Engelbrektson, A., Kunin, V., Wrighton, K. C., Zvenigorodsky, N., Chen, F., Ochman, H., & Hugenholtz, P. (2010) · The ISME Journal · doi:10.1038/ismej.2009.153 · Cited by 593
Interspecific combative interactions between wood-decaying basidiomycetes
Boddy, L. (2000) · FEMS Microbiology Ecology · doi:10.1016/s0168-6496(99)00093-8 · Cited by 577
Bias and artifacts in multitemplate polymerase chain reactions (PCR)
Kanagawa, T. (2003) · Journal of Bioscience and Bioengineering · doi:10.1016/s1389-1723(03)90130-7 · Cited by 566
Öpik, M., Metsis, M., Daniell, T. J., Zobel, M., & Moora, M. (2009) · New Phytologist · doi:10.1111/j.1469-8137.2009.02920.x · Cited by 557
Tedersoo, L., Nilsson, R. H., Abarenkov, K., Jairus, T., Sadam, A., Saar, I., Bahram, M., Bechem, E., Chuyong, G., & Kõljalg, U. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03373.x · Cited by 549
Self-citationBarcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification
Berry, D., Ben Mahfoudh, K., Wagner, M., & Loy, A. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.05220-11 · Cited by 518
AMEND, A. S., SEIFERT, K. A., & BRUNS, T. D. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04898.x · Cited by 515
Sequencing our way towards understanding global eukaryotic biodiversity
Bik, H. M., Porazinska, D. L., Creer, S., Caporaso, J. G., Knight, R., & Thomas, W. K. (2012) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2011.11.010 · Cited by 491
VAN TUINEN, D., JACQUOT, E., ZHAO, B., GOLLOTTE, A., & GIANINAZZI‐PEARSON, V. (1998) · Molecular Ecology · doi:10.1046/j.1365-294x.1998.00410.x · Cited by 464
Tedersoo, L., Jairus, T., Horton, B. M., Abarenkov, K., Suvi, T., Saar, I., & Kõljalg, U. (2008) · New Phytologist · doi:10.1111/j.1469-8137.2008.02561.x · Cited by 447
Self-citationJumpponen, A., & Jones, K. L. (2009) · New Phytologist · doi:10.1111/j.1469-8137.2009.02990.x · Cited by 432
Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T‐RFLP analysis
Dickie, I. A., Xu, B., & Koide, R. T. (2002) · New Phytologist · doi:10.1046/j.1469-8137.2002.00535.x · Cited by 430
Current state and perspectives of fungal DNA barcoding and rapid identification procedures
Begerow, D., Nilsson, H., Unterseher, M., & Maier, W. (2010) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-010-2585-4 · Cited by 402
Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide
Coleman, A. W. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.10.008 · Cited by 397
Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification
Berry, D., Ben Mahfoudh, K., Wagner, M., & Loy, A. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.07448-11 · Cited by 394
Krüger, M., Stockinger, H., Krüger, C., & Schüßler, A. (2009) · New Phytologist · doi:10.1111/j.1469-8137.2009.02835.x · Cited by 389
Gihring, T. M., Green, S. J., & Schadt, C. W. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02550.x · Cited by 385
Gollotte, A., van Tuinen, D., & Atkinson, D. (2004) · Mycorrhiza · doi:10.1007/s00572-003-0244-7 · Cited by 377
TABERLET, P., PRUD’HOMME, S. M., CAMPIONE, E., ROY, J., MIQUEL, C., SHEHZAD, W., GIELLY, L., RIOUX, D., CHOLER, P., CLÉMENT, J., et al. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2011.05317.x · Cited by 353
Parameswaran, P., Jalili, R., Tao, L., Shokralla, S., Gharizadeh, B., Ronaghi, M., & Fire, A. Z. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm760 · Cited by 344
Fast, accurate error-correction of amplicon pyrosequences using Acacia
Bragg, L., Stone, G., Imelfort, M., Hugenholtz, P., & Tyson, G. W. (2012) · Nature Methods · doi:10.1038/nmeth.1990 · Cited by 337
Hartmann, M., Howes, C. G., VanInsberghe, D., Yu, H., Bachar, D., Christen, R., Henrik Nilsson, R., Hallam, S. J., & Mohn, W. W. (2012) · The ISME Journal · doi:10.1038/ismej.2012.84 · Cited by 320
DNA barcoding of arbuscular mycorrhizal fungi
Stockinger, H., Krüger, M., & Schüßler, A. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03262.x · Cited by 319
Yeast Pre-rRNA Processing and Modification Occur Cotranscriptionally
Koš, M., & Tollervey, D. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.02.024 · Cited by 308
Nilsson, R. H., Ryberg, M., Abarenkov, K., Sjökvist, E., & Kristiansson, E. (2009) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2009.01618.x · Cited by 307
Self-citationAbarenkov, K., Tedersoo, L., Nilsson, R. H., Vellak, K., Saar, I., Veldre, V., Parmasto, E., Prous, M., Aan, A., Ots, M., et al. (2010) · Evolutionary Bioinformatics · doi:10.4137/ebo.s6271 · Cited by 301
Self-citationFaircloth, B. C., & Glenn, T. C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042543 · Cited by 289
Tanner, M. A., Goebel, B. M., Dojka, M. A., & Pace, N. R. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.8.3110-3113.1998 · Cited by 270
Representative sampling for reliable data analysis: Theory of Sampling
Petersen, L., Minkkinen, P., & Esbensen, K. H. (2005) · Chemometrics and Intelligent Laboratory Systems · doi:10.1016/j.chemolab.2004.09.013 · Cited by 266
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
Hao, X., Jiang, R., & Chen, T. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq725 · Cited by 262
BEAMing up for detection and quantification of rare sequence variants
Li, M., Diehl, F., Dressman, D., Vogelstein, B., & Kinzler, K. W. (2006) · Nature Methods · doi:10.1038/nmeth850 · Cited by 261
Prosser, J. I. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02201.x · Cited by 251
Adding unaligned sequences into an existing alignment using MAFFT and LAST
Katoh, K., & Frith, M. C. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts578 · Cited by 241
GAZIS, R., REHNER, S., & CHAVERRI, P. (2011) · Molecular Ecology · doi:10.1111/j.1365-294x.2011.05110.x · Cited by 219
Evidence that chytrids dominate fungal communities in high-elevation soils
Freeman, K. R., Martin, A. P., Karki, D., Lynch, R. C., Mitter, M. S., Meyer, A. F., Longcore, J. E., Simmons, D. R., & Schmidt, S. K. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907303106 · Cited by 205
RNA reveals a succession of active fungi during the decay of Norway spruce logs
Rajala, T., Peltoniemi, M., Hantula, J., Mäkipää, R., & Pennanen, T. (2011) · Fungal Ecology · doi:10.1016/j.funeco.2011.05.005 · Cited by 200
Self-citationAccurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes
Liu, K.-L., Porras-Alfaro, A., Kuske, C. R., Eichorst, S. A., & Xie, G. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.06826-11 · Cited by 195
Lindahl, B. D., de Boer, W., & Finlay, R. D. (2010) · The ISME Journal · doi:10.1038/ismej.2010.19 · Cited by 192
Self-citationBödeker, I. T. M., Nygren, C. M. R., Taylor, A. F. S., Olson, Å., & Lindahl, B. D. (2009) · The ISME Journal · doi:10.1038/ismej.2009.77 · Cited by 190
Self-citationStrain-Dependent Variation in 18S Ribosomal DNA Copy Numbers in Aspergillus fumigatus
Herrera, M. L., Vallor, A. C., Gelfond, J. A., Patterson, T. F., & Wickes, B. L. (2009) · Journal of Clinical Microbiology · doi:10.1128/jcm.02073-08 · Cited by 189
Lahr, D. J. G., & Katz, L. A. (2009) · BioTechniques · doi:10.2144/000113219 · Cited by 189
Estimation of fungal biomass in forest litter and soil
Baldrian, P., Větrovský, T., Cajthaml, T., Dobiášová, P., Petránková, M., Šnajdr, J., & Eichlerová, I. (2013) · Fungal Ecology · doi:10.1016/j.funeco.2012.10.002 · Cited by 184
Carlsen, T., Aas, A. B., Lindner, D., Vrålstad, T., Schumacher, T., & Kauserud, H. (2012) · Fungal Ecology · doi:10.1016/j.funeco.2012.06.003 · Cited by 180
Self-citationLindner, D. L., & Banik, M. T. (2011) · Mycologia · doi:10.3852/10-331 · Cited by 170
Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities
Bazzicalupo, A. L., Bálint, M., & Schmitt, I. (2013) · Fungal Ecology · doi:10.1016/j.funeco.2012.09.003 · Cited by 166
Lekberg, Y., Schnoor, T. K., Kjøller, R., Gibbons, S. M., Hansen, L. H., Al‐Soud, W. A., Sørensen, S. J., & Rosendahl, S. (2011) · Journal of Ecology · doi:10.1111/j.1365-2745.2011.01894.x · Cited by 160
Self-citationInsidious effects of sequencing errors on perceived diversity in molecular surveys
Dickie, I. A. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03473.x · Cited by 157
Huber, J. A., Morrison, H. G., Huse, S. M., Neal, P. R., Sogin, M. L., & Welch, D. B. M. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01857.x · Cited by 151
Denoising PCR-amplified metagenome data
Rosen, M., Callahan, B. J., Fisher, D. S., & Holmes, S. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-283 · Cited by 140
Population genetics of ectomycorrhizal fungi: from current knowledge to emerging directions
Douhan, G. W., Vincenot, L., Gryta, H., & Selosse, M. (2011) · Fungal Biology · doi:10.1016/j.funbio.2011.03.005 · Cited by 140
Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses
Fonseca, V. G., Nichols, B., Lallias, D., Quince, C., Carvalho, G. R., Power, D. M., & Creer, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks002 · Cited by 137
Arbuscular Mycorrhiza: The Challenge to Understand the Genetics of the Fungal Partner
Sanders, I. R., & Croll, D. (2010) · Annual Review of Genetics · doi:10.1146/annurev-genet-102108-134239 · Cited by 135
Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets
Gobet, A., Quince, C., & Ramette, A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq545 · Cited by 127
Nilsson, R. H., Tedersoo, L., Lindahl, B. D., Kjøller, R., Carlsen, T., Quince, C., Abarenkov, K., Pennanen, T., Stenlid, J., Bruns, T. D., et al. (2011) · New Phytologist · doi:10.1111/j.1469-8137.2011.03755.x · Cited by 124
Self-citationDavey, M. L., Heegaard, E., Halvorsen, R., Ohlson, M., & Kauserud, H. (2012) · New Phytologist · doi:10.1111/j.1469-8137.2012.04215.x · Cited by 120
Self-citationFungi Unearthed: Transcripts Encoding Lignocellulolytic and Chitinolytic Enzymes in Forest Soil
Kellner, H., & Vandenbol, M. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010971 · Cited by 117
Hartmann, M., Howes, C. G., Abarenkov, K., Mohn, W. W., & Nilsson, R. H. (2010) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2010.08.008 · Cited by 117
Self-citationPorter, T. M., & Golding, G. B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035749 · Cited by 87
Bengtsson‐Palme, J., Eriksson, K. M., Hartmann, M., Wang, Z., Shenoy, B. D., Grelet, G., Abarenkov, K., Petri, A., Rosenblad, M. A., & Nilsson, R. H. (2011) · Antonie van Leeuwenhoek · doi:10.1007/s10482-011-9598-6 · Cited by 83
Self-citationThe Promise and Pitfalls of Sequence-Based Identification of Plant-Pathogenic Fungi and Oomycetes
Kang, S., Mansfield, M. A., Park, B.-S., Geiser, D. M., Ivors, K., Coffey, M. D., Grünwald, N. J., Martin, F. N., Lévesque, C. A., & Blair, J. E. (2010) · Phytopathology · doi:10.1094/phyto-100-8-0732 · Cited by 83
Systematic exploration of error sources in pyrosequencing flowgram data
Balzer, S., Malde, K., & Jonassen, I. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr251 · Cited by 81
Pennanen, T., Caul, S., Daniell, T. J., et al. (2004) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2004.01.014 · Cited by 78
Self-citationChristen, R. (2008) · Microbes and Environments · doi:10.1264/jsme2.me08525 · Cited by 76
Kumar, S., Carlsen, T., Mevik, B., Enger, P., Blaalid, R., Shalchian‐Tabrizi, K., & Kauserud, H. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-182 · Cited by 75
Self-citationHigh consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples
Kauserud, H., Kumar, S., Brysting, A. K., Nordén, J., & Carlsen, T. (2011) · Mycorrhiza · doi:10.1007/s00572-011-0403-1 · Cited by 71
Self-citationGrant, S. M., Grant, W. D., Cowan, D. A., et al. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.1.135-143.2006 · Cited by 70
Kerekes, J. F., Kaspari, M. E., Stevenson, B. S., Nilsson, R. H., Hartmann, M., Amend, A. S., & Bruns, T. D. (2013) · Molecular Ecology · doi:10.1111/mec.12259 · Cited by 64
Self-citationTedersoo, L., Abarenkov, K., Nilsson, R. H., Schüßler, A., Grelet, G., Kohout, P., Oja, J., Bonito, G. M., Veldre, V., Jairus, T., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024940 · Cited by 60
Self-citationA grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences
Russell, D. J., Way, S. F., Benson, A. K., & Sayood, K. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-601 · Cited by 42
Determination of mRNA half-lives inCandida albicansusing thiolutin as a transcription inhibitor
Kebaara, B. W., Nielsen, L. E., Nickerson, K. W., & Atkin, A. L. (2006) · Genome · doi:10.1139/g06-046 · Cited by 24
Metagenomics for Study of Fungal Ecology
Lindahl, B. D., & Kuske, C. R. (2013) · Wiley eBooks · doi:10.1002/9781118735893.ch13 · Cited by 21
Self-citation
Cited by
Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community
Raja, H. A., Miller, A. N., Pearce, C. J., & Oberlies, N. H. (2017) · Journal of Natural Products · doi:10.1021/acs.jnatprod.6b01085 · Cited by 931
Freschet, G. T., Pagès, L., Iversen, C. M., Comas, L. H., Rewald, B., Roumet, C., Klimešová, J., Zadworny, M., Poorter, H., Postma, J. A., et al. (2021) · New Phytologist · doi:10.1111/nph.17572 · Cited by 668
Smith, D. P., & Peay, K. G. (2014) · PLoS ONE · doi:10.1371/journal.pone.0090234 · Cited by 553
Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies
Op De Beeck, M., Lievens, B., Busschaert, P., Declerck, S., Vangronsveld, J., & Colpaert, J. V. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097629 · Cited by 538
Fernandez, C. W., & Kennedy, P. G. (2016) · New Phytologist · doi:10.1111/nph.13648 · Cited by 532
Metadata
- Authors
- Lindahl, B. D., Nilsson, R. H., Tedersoo, L., Abarenkov, K., Carlsen, T., Kjøller, R., Kõljalg, U., Pennanen, T., Rosendahl, S., Stenlid, J., & Kauserud, H.
- Venue
- New Phytologist
- Publisher
- Wiley
- Published
- 2013-03-28
- Volume
- 199
- Issue
- 1
- Pages
- 288-299
- ISSN
- 0028-646X (ISSN-L)
- 1469-8137
- OpenAlex
- W2095667786
- Cited by
- 892
- References
- 108
- FWCI
- 82.65
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
