The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
Open accessOverview
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
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
UPARSE: highly accurate OTU sequences from microbial amplicon reads
Edgar, R. C. (2013) · Nature Methods · doi:10.1038/nmeth.2604 · Cited by 16,707
A Direct Approach to False Discovery Rates
Storey, J. D. (2002) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/1467-9868.00346 · Cited by 5,603
McDonald, D., Price, M. N., Goodrich, J., Nawrocki, E. P., DeSantis, T. Z., Probst, A., Andersen, G. L., Knight, R., & Hugenholtz, P. (2012) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,064
Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00335-09 · Cited by 4,063
Self-citationGlobal diversity and geography of soil fungi
Tedersoo, L., Bahram, M., Põlme, S., Kõljalg, U., Yorou, N. S., Wijesundera, R., Ruiz, L. V., Vasco-Palacios, A. M., Thu, P. Q., Suija, A., et al. (2014) · Science · doi:10.1126/science.1256688 · Cited by 3,702
Methods of Soil Analysis 2d ed., pt. 1; Physical and Mineralogical Methods
Klute, A. (1988) · Soil Science · doi:10.1097/00010694-198808000-00014 · Cited by 3,145
The 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
Pyrosequencing enumerates and contrasts soil microbial diversity
Roesch, L. F. W., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H., Camargo, F. A. O., Farmerie, W. G., & Triplett, E. W. (2007) · The ISME Journal · doi:10.1038/ismej.2007.53 · Cited by 1,852
Leff, J. W., Jones, S. E., Prober, S. M., Barberán, A., Borer, E. T., Firn, J. L., Harpole, W. S., Hobbie, S. E., Hofmockel, K. S., Knops, J. M. H., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1508382112 · Cited by 1,452
Self-citationUnusual biology across a group comprising more than 15% of domain Bacteria
Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H., & Banfield, J. F. (2015) · Nature · doi:10.1038/nature14486 · Cited by 1,216 · cited 1×
“These 37 methods have advanced our understanding of terrestrial microbiology in a myriad of 38 ways, by: i) revealing that thousands of unique microbial taxa can inhabit a single gram 39 of soil (1-3); ii) uncovering novel soil microbial diversity (4, 5); and iii) identifying putative 40 functions of uncultivated taxa…”
BackgroundComputational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil
Gans, J., Wolinsky, M., & Dunbar, J. (2005) · Science · doi:10.1126/science.1112665 · Cited by 1,207
A critical review on the role of mycorrhizal fungi in the uptake of phosphorus by plants
Bolan, N. S. (1991) · Plant and Soil · doi:10.1007/bf00012037 · Cited by 1,188
Nocker, A., Cheung, C.-Y., & Camper, A. K. (2006) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2006.04.015 · Cited by 1,073
The bacterial biogeography of British soils
Griffiths, R. I., Thomson, B. C., James, P., Bell, T., Bailey, M., & Whiteley, A. S. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02480.x · Cited by 901
Blazewicz, S. J., Barnard, R. L., Daly, R. A., & Firestone, M. K. (2013) · The ISME Journal · doi:10.1038/ismej.2013.102 · Cited by 878
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
Mackelprang, R., Waldrop, M. P., DeAngelis, K. M., David, M. M., Chavarria, K. L., Blazewicz, S. J., Rubin, E. M., & Jansson, J. K. (2011) · Nature · doi:10.1038/nature10576 · Cited by 711
Release and persistence of extracellular DNA in the environment
Nielsen, K. M., Johnsen, P. J., Bensasson, D., & Daffonchio, D. (2007) · Environmental Biosafety Research · doi:10.1051/ebr:2007031 · Cited by 614
Extracellular DNA in soil and sediment: fate and ecological relevance
Pietramellara, G., Ascher, J., Borgogni, F., Ceccherini, M. T., Guerri, G., & Nannipieri, P. (2009) · Biology and Fertility of Soils · doi:10.1007/s00374-008-0345-8 · Cited by 596
Use of Propidium Monoazide for Live/Dead Distinction in Microbial Ecology
Nocker, A., Sossa-Fernandez, P., Burr, M. D., & Camper, A. K. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02987-06 · Cited by 577
Fierer, N., Breitbart, M., Nulton, J., Salamon, P., Lozupone, C., Jones, R., Robeson, M., Edwards, R. A., Felts, B., Rayhawk, S., et al. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00358-07 · Cited by 563
Self-citationCycling of extracellular DNA in the soil environment
Levy-Booth, D. J., Campbell, R. G., Gulden, R. H., Hart, M. M., Powell, J. R., Klironomos, J. N., Pauls, K. P., Swanton, C. J., Trevors, J. T., & Dunfield, K. E. (2007) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2007.06.020 · Cited by 523
Discovery of novel intermediate forms redefines the fungal tree of life
Jones, M. D. M., Forn, I., Gadelha, C., Egan, M. J., Bass, D., Massana, R., & Richards, T. A. (2011) · Nature · doi:10.1038/nature09984 · Cited by 425
Fittipaldi, M., Nocker, A., & Codony, F. (2012) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2012.08.007 · Cited by 425
Ramirez, K. S., Leff, J. W., Barberán, A., Bates, S. T., Betley, J., Crowther, T. W., Kelly, E. F., Oldfield, E. E., Shaw, E. A., Steenbock, C., et al. (2014) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2014.1988 · Cited by 423
Self-citationRocca, J. D., Hall, E. K., Lennon, J. T., Evans, S. E., Waldrop, M. P., Cotner, J. B., Nemergut, D. R., Graham, E. B., & Wallenstein, M. D. (2015) · The ISME Journal · doi:10.1038/ismej.2014.252 · Cited by 398
Extracellular DNA Plays a Key Role in Deep-Sea Ecosystem Functioning
Dell'Anno, A., & Danovaro, R. (2005) · Science · doi:10.1126/science.1117475 · Cited by 378
Durfee, T., Nelson, R., Baldwin, S., Plunkett, G., Burland, V., Mau, B., Petrosino, J. F., Qin, X., Muzny, D. M., Ayele, M., et al. (2008) · Journal of Bacteriology · doi:10.1128/jb.01695-07 · Cited by 371
Dead or Alive: Molecular Assessment of Microbial Viability
Cangelosi, G. A., & Meschke, J. S. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.01763-14 · Cited by 339
Agnelli, A., Ascher, J., Corti, G., Ceccherini, M. T., Nannipieri, P., & Pietramellara, G. (2004) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2004.02.004 · Cited by 332
Tackling soil diversity with the assembly of large, complex metagenomes
Howe, A. C., Jansson, J. K., Malfatti, S. A., Tringe, S. G., Tiedje, J. M., & Brown, C. T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1402564111 · Cited by 321
Nucleic Acids and Proteins in Soil
(2006) · Soil Biology · doi:10.1007/3-540-29449-x · Cited by 201
Strain-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
Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene
Coolen, M. J. L., Orsi, W. D., Balkema, C., Quince, C., Harris, K., Sylva, S. P., Filipova-Marinova, M., & Giosan, L. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219283110 · Cited by 182
DNA adsorption to soils and sediments
Ogram, A., Sayler, G. S., Gustin, D., & Lewis, R. J. (1988) · Environmental Science & Technology · doi:10.1021/es00173a020 · Cited by 172
Wertz, S., Leigh, A. K. K., & Grayston, S. J. (2012) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2011.01204.x · Cited by 170
Nocker, A., Richter‐Heitmann, T., Montijn, R. C., Schuren, F. H. J., & Kort, R. (2010) · PubMed · doi:10.2436/20.1501.01.111 · Cited by 130
Docherty, K. M., Borton, H. M., Espinosa, N. J., Farella, M. M., Gil-Loaiza, J., Gutknecht, J., Maes, P. W., Mott, B. M., Parnell, J., Purdy, G., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135352 · Cited by 124
MICROBIAL SURVIVAL: The Paleome: A Sedimentary Genetic Record of Past Microbial Communities
Inagaki, F., Okada, H., Tsapin, A. I., & Nealson, K. H. (2005) · Astrobiology · doi:10.1089/ast.2005.5.141 · Cited by 95
Evaluation of viability-qPCR detection system on viable and dead Salmonella serovar Enteritidis
Barbau-Piednoir, E., Mahillon, J., Pillyser, J., Coucke, W., Roosens, N. H. C., & Botteldoorn, N. (2014) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2014.06.003 · Cited by 88
Wagner, A. O., Praeg, N., Reitschuler, C., et al. (2015) · Applied Soil Ecology · doi:10.1016/j.apsoil.2015.04.005 · Cited by 88
Stabilization of Extracellular DNA and Proteins by Transient Binding to Various Soil Components
Nielsen, K. M., Calamai, L., & Pietramellara, G. (2006) · Springer eBooks · doi:10.1007/3-540-29449-x_7 · Cited by 83
Dlott, G. A., Maul, J. E., Buyer, J. S., & Yarwood, S. A. (2015) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2015.05.027 · Cited by 62
Zhang, X., Barberán, A., Zhu, X., Zhang, G., & Han, X. (2014) · PLoS ONE · doi:10.1371/journal.pone.0115798 · Cited by 14
Cited by
Microbiome definition re-visited: old concepts and new challenges
Berg, G., Rybakova, D., Fischer, D., Cernava, T., Vergès, M.-C. C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Corral, G. H., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00875-0 · Cited by 2,275
Best practices for analysing microbiomes
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030
Hu, L., Robert, C. A. M., Cadot, S., Zhang, X., Ye, M., Li, B., Manzo, D., Chervet, N., Steinger, T., van der Heijden, M. G. A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05122-7 · Cited by 1,626
Soil nematode abundance and functional group composition at a global scale
van den Hoogen, J., Geisen, S., Routh, D., Ferris, H., Traunspurger, W., Wardle, D. A., de Goede, R. G. M., Adams, B. J., Ahmad, W., Andriuzzi, W. S., et al. (2019) · Nature · doi:10.1038/s41586-019-1418-6 · Cited by 1,292
Life and death in the soil microbiome: how ecological processes influence biogeochemistry
Sokol, N. W., Slessarev, E., Marschmann, G. L., Nicolas, A., Blazewicz, S. J., Brodie, E. L., Firestone, M. K., Foley, M. M., Hestrin, R., Hungate, B. A., et al. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00695-z · Cited by 1,179
Metadata
- Authors
- Carini, P., Marsden, P. J., Leff, J. W., Morgan, E. E., Strickland, M. S., & Fierer, N.
- Venue
- Nature Microbiology
- Published
- 2016-12-19
- Volume
- 2
- Issue
- 3
- Pages
- 16242-16242
- ISSN
- 2058-5276 (ISSN-L)
- OpenAlex
- W2950635704
- Cited by
- 1,040
- References
- 45
- FWCI
- 76.38
- 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.