Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

Performance of cytochrome c oxidase subunit I (COI), ribosomal DNA Large Subunit (LSU) and Internal Transcribed Spacer 2 (ITS2) in DNA barcoding of Collembola

(2015) Sten Anslan et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

(2015) Leho Tedersoo et al.   MycoKeys

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

(2014) B. E. Deagle et al.   Biology Letters

A quantitative analysis of species sorting across organisms and ecosystems

(2014) Janne Soininen   ECOLOGY

Do diverse overstoreys induce diverse understoreys? Lessons learnt from an experimental–observational platform in Finland

(2014) E. Ampoorter et al.   FOREST ECOLOGY AND MANAGEMENT

When the forest dies: the response of forest soil fungi to a bark beetle-induced tree dieback

(2014) Martina Štursová et al.   ISME Journal

Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses

(2014) Leho Tedersoo et al.   MOLECULAR ECOLOGY

Does host plant richness explain diversity of ectomycorrhizal fungi? Re-evaluation of Gaoet al. (2013) data sets reveals sampling effects

(2014) Leho Tedersoo et al.   MOLECULAR ECOLOGY

AssessingSymbiodiniumdiversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region

(2014) Chatchanit Arif et al.   MOLECULAR ECOLOGY

Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps

(2014) L. Pellissier et al.   MOLECULAR ECOLOGY

Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach

(2014) Guillaume Lentendu et al.   MOLECULAR ECOLOGY

Pathogens and insect herbivores drive rainforest plant diversity and composition

(2014) Robert Bagchi et al.   NATURE

Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass

(2014) Inga Hiiesalu et al.   NEW PHYTOLOGIST

Global biogeography ofAlnus-associatedFrankiaactinobacteria

(2014) Sergei Põlme et al.   NEW PHYTOLOGIST

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Much beyond Mantel: Bringing Procrustes Association Metric to the Plant and Soil Ecologist’s Toolbox

(2014) Francy Junio Gonçalves Lisboa et al.   PLoS One

Soil biodiversity and soil community composition determine ecosystem multifunctionality

(2014) C. Wagg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

(2014) K. S. Ramirez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Tree species influence on microbial communities in litter and soil: Current knowledge and research needs

(2013) Cindy E. Prescott et al.   FOREST ECOLOGY AND MANAGEMENT

Tree species effects on nutrient cycling and soil biota: A feedback mechanism favouring species coexistence

(2013) Cristina Aponte et al.   FOREST ECOLOGY AND MANAGEMENT

Is the effect of trees on soil properties mediated by soil fauna? A case study from post-mining sites

(2013) Jan Frouz et al.   FOREST ECOLOGY AND MANAGEMENT

Global drivers and patterns of microbial abundance in soil

(2013) Hector M. Serna-Chavez et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Strong coupling of plant and fungal community structure across western Amazonian rainforests

(2013) Kabir G Peay et al.   ISME Journal

The distance decay of similarity in communities of ectomycorrhizal fungi in different ecosystems and scales

(2013) Mohammad Bahram et al.   JOURNAL OF ECOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils

(2013) Darren S. Baldwin et al.   MOLECULAR ECOLOGY

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Biogeography of ectomycorrhizal fungi associated with alders (Alnusspp.) in relation to biotic and abiotic variables at the global scale

(2013) Sergei Põlme et al.   NEW PHYTOLOGIST

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Shedding new light on the diet of Norwegian lemmings: DNA metabarcoding of stomach content

(2013) Eeva M. Soininen et al.   POLAR BIOLOGY

Plant diversity effects on soil food webs are stronger than those of elevated CO2 and N deposition in a long-term grassland experiment

(2013) N. Eisenhauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest

(2013) K. E. Clemmensen et al.   SCIENCE

Higher levels of multiple ecosystem services are found in forests with more tree species

(2013) Lars Gamfeldt et al.   Nature Communications

Designing forest biodiversity experiments: general considerations illustrated by a new large experiment in subtropical China

(2013) Helge Bruelheide et al.   Methods in Ecology and Evolution

Lineages of ectomycorrhizal fungi revisited: Foraging strategies and novel lineages revealed by sequences from belowground

(2013) Leho Tedersoo et al.   Fungal Biology Reviews

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Biodiversity effects on ecosystem functioning change along environmental stress gradients

(2012) Bastian Steudel et al.   ECOLOGY LETTERS

Plant diversity controls arthropod biomass and temporal stability

(2012) Elizabeth T. Borer et al.   ECOLOGY LETTERS

COEVOLUTION AND THE ARCHITECTURE OF MUTUALISTIC NETWORKS

(2012) Scott L. Nuismer et al.   EVOLUTION

Global biogeography of highly diverse protistan communities in soil

(2012) Scott T Bates et al.   ISME Journal

Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

(2012) Charles Bachy et al.   ISME Journal

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

Enzymatic activities and stable isotope patterns of ectomycorrhizal fungi in relation to phylogeny and exploration types in an afrotropical rain forest

(2012) Leho Tedersoo et al.   NEW PHYTOLOGIST

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impacts of Biodiversity Loss Escalate Through Time as Redundancy Fades

(2012) P. B. Reich et al.   SCIENCE

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

The functional role of producer diversity in ecosystems

(2011) Bradley J. Cardinale et al.   AMERICAN JOURNAL OF BOTANY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Belowground biodiversity effects of plant symbionts support aboveground productivity

(2011) Cameron Wagg et al.   ECOLOGY LETTERS

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian et al.   ISME Journal

Regional and local patterns of ectomycorrhizal fungal diversity and community structure along an altitudinal gradient in the Hyrcanian forests of northern Iran

(2011) Mohammad Bahram et al.   NEW PHYTOLOGIST

The local-regional species richness relationship: new perspectives on the null-hypothesis

(2011) Robert C. Szava-Kovats et al.   OIKOS

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition

(2010) Jaroslav Šnajdr et al.   FEMS MICROBIOLOGY ECOLOGY

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

(2010) Anthony A Chariton et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

Genetic variation and phylogeny of Scandinavian species of Grania (Annelida: Clitellata: Enchytraeidae), with the discovery of a cryptic species

(2010) Pierre De Wit et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

(2010) RALPH MEDINGER et al.   MOLECULAR ECOLOGY

Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment

(2010) Christoph Scherber et al.   NATURE

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals

(2010) Hui Yao et al.   PLoS One

Is forest diversity driving ecosystem function and service?

(2010) Karin Nadrowski et al.   Current Opinion in Environmental Sustainability

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere

(2009) A. Jumpponen et al.   NEW PHYTOLOGIST

The ITS2 Database III—sequences and structures for phylogeny

(2009) Christian Koetschan et al.   NUCLEIC ACIDS RESEARCH

Tree Species Traits Influence Soil Physical, Chemical, and Biological Properties in High Elevation Forests

(2009) Edward Ayres et al.   PLoS One

Partitioning the effects of biodiversity and environmental heterogeneity for productivity and mortality in a tropical tree plantation

(2008) Chrystal Healy et al.   JOURNAL OF ECOLOGY

Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide

(2008) Annette W. Coleman   MOLECULAR PHYLOGENETICS AND EVOLUTION

Effects of stand tree species composition and diversity on abundance of predatory arthropods

(2008) Harri Vehviläinen et al.   OIKOS

Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil

(2008) Jaroslav Šnajdr et al.   SOIL BIOLOGY & BIOCHEMISTRY