Journal ArticleDOI
The UNITE database for molecular identification of fungi - recent updates and future perspectives
Kessy Abarenkov,R. Henrik Nilsson,R. Henrik Nilsson,Karl-Henrik Larsson,Ian J. Alexander,Ursula Eberhardt,Susanne Erland,Klaus Høiland,Rasmus Kjøller,Ellen Larsson,Taina Pennanen,Robin Sen,Andy F. S. Taylor,Leho Tedersoo,Björn M. Ursing,Trude Vrålstad,Kare Liimatainen,Ursula Peintner,Urmas Kõljalg +18 more
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This article is published in New Phytologist.The article was published on 2010-04-01. It has received 1471 citations till now.read more
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Towards a unified paradigm for sequence-based identification of fungi
Urmas Kõljalg,Urmas Kõljalg,R. Henrik Nilsson,Kessy Abarenkov,Leho Tedersoo,Andy F. S. Taylor,Andy F. S. Taylor,Mohammad Bahram,Scott T. Bates,Thomas D. Bruns,Johan Bengtsson-Palme,Tony M. Callaghan,Brian Douglas,Tiia Drenkhan,Ursula Eberhardt,Margarita Dueñas,Tine Grebenc,Gareth W. Griffith,Martin Hartmann,Paul M. Kirk,Petr Kohout,Petr Kohout,Ellen Larsson,Björn D. Lindahl,Robert Lücking,María P. Martín,P. Brandon Matheny,Nhu H. Nguyen,Tuula Niskanen,Jane Oja,Kabir G. Peay,Ursula Peintner,Marko Peterson,Kadri Põldmaa,Lauri Saag,Irja Saar,Arthur Schüßler,James A. Scott,Carolina Senés,Matthew E. Smith,Ave Suija,Ave Suija,D. Lee Taylor,M. Teresa Telleria,Michael Weiss,Karl-Henrik Larsson +45 more
TL;DR: All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type, and the term ‘species hypothesis’ (SH) is introduced for the taxa discovered in clustering on different similarity thresholds.
Journal ArticleDOI
FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild
Nhu H. Nguyen,Zewei Song,Scott T. Bates,Sara Branco,Leho Tedersoo,Jon Menke,Jonathan S. Schilling,Peter G. Kennedy +7 more
TL;DR: Fungi typically live in highly diverse communities composed of multiple ecological guilds, and FUNGuild is a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline.
Journal ArticleDOI
Environmental DNA metabarcoding: transforming how we survey animal and plant communities
Kristy Deiner,Holly M. Bik,Elvira Mächler,Elvira Mächler,Mathew Seymour,Anaïs Lacoursière-Roussel,Florian Altermatt,Florian Altermatt,Simon Creer,Iliana Bista,Iliana Bista,David M. Lodge,Natasha de Vere,Michael E. Pfrender,Louis Bernatchez +14 more
TL;DR: The use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance are reviewed, which distill what is known about the ability of different eDNA sample types to approximate richness in space and across time.
Journal ArticleDOI
Distinct soil microbial diversity under long-term organic and conventional farming
TL;DR: The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.
Journal ArticleDOI
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe
Jonathan W. Leff,Stuart E. Jones,Suzanne M. Prober,Albert Barberán,Elizabeth T. Borer,Jennifer Firn,W. Stanley Harpole,Sarah E. Hobbie,Kirsten S. Hofmockel,Johannes M. H. Knops,Rebecca L. McCulley,Kimberly J. La Pierre,Anita C. Risch,Eric W. Seabloom,Martin Schütz,Christopher M. Steenbock,Carly J. Stevens,Noah Fierer +17 more
TL;DR: The results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of faster-growing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.
References
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Genome sequencing in microfabricated high-density picolitre reactors
Marcel Margulies,Michael Egholm,William E. Altman,Said Attiya,Joel S. Bader,Lisa A. Bemben,Jan Berka,Michael S. Braverman,Yi-Ju Chen,Zhoutao Chen,Scott Dewell,Lei Du,J. M. Fierro,Xavier V. Gomes,Brian C. Godwin,Wen He,Scott Edward Helgesen,Chun Heen Ho,Gerard P. Irzyk,Szilveszter C. Jando,Maria L. I. Alenquer,Thomas P. Jarvie,Kshama B. Jirage,Jong-Bum Kim,James R. Knight,Janna R. Lanza,John H. Leamon,Steven Lefkowitz,Ming Lei,Jing Li,Kenton Lohman,Hong Lu,Vinod Makhijani,Keith Mcdade,Michael P. McKenna,Eugene W. Myers,Elizabeth Nickerson,John Nobile,Ramona Plant,Bernard P. Puc,Michael T. Ronan,George T. Roth,Gary J. Sarkis,Jan Fredrik Simons,John Simpson,Maithreyan Srinivasan,Karrie R. Tartaro,Alexander Tomasz,Kari A. Vogt,Greg A. Volkmer,Shally H. Wang,Yong Wang,Michael P. Weiner,Pengguang Yu,Richard F. Begley,Jonathan M. Rothberg +55 more
TL;DR: A scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments with 96% coverage at 99.96% accuracy in one run of the machine is described.
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Temperature sensitivity of soil carbon decomposition and feedbacks to climate change
TL;DR: This work has suggested that several environmental constraints obscure the intrinsic temperature sensitivity of substrate decomposition, causing lower observed ‘apparent’ temperature sensitivity, and these constraints may, themselves, be sensitive to climate.
Journal ArticleDOI
Next-generation DNA sequencing.
Jay Shendure,Hanlee P. Ji +1 more
TL;DR: Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.
Journal ArticleDOI
UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi
Urmas Kõljalg,Karl-Henrik Larsson,Kessy Abarenkov,R. Henrik Nilsson,Ian J. Alexander,Ursula Eberhardt,Susanne Erland,Klaus Høiland,Rasmus Kjøller,Ellen Larsson,Taina Pennanen,Robin Sen,Andy F. S. Taylor,Leho Tedersoo,Trude Vrålstad,Björn M. Ursing +15 more
TL;DR: The UNITE database, an open-access database dedicated to the reliable identification of ECM fungi, comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full her barium reference identification data, collector/source and ecological data.
Journal ArticleDOI
Review: Factors affecting rhizosphere priming effects
TL;DR: It was concluded that root growth dynamics and photosynthesis intensity are the most important plant-mediated factors affecting RPE.
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