A DNA-barcode biodiversity standard analysis method (DNA-BSAM) reveals a large variance in the effect of a range of biological, chemical and physical soil management interventions at different sites, but location is one of the most important aspects determining the nature of agricultural soil microbiology

Inconsistent effects of agricultural practices on soil fungal communities across twelve European long‐term experiments

(2021) S. E. Hannula et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

A conceptual guide to measuring species diversity

(2021) Michael Roswell et al.   OIKOS

The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks

(2021) Hiroki Morita et al.   PLoS One

Blind spots in global soil biodiversity and ecosystem function research

(2020) Carlos A. Guerra et al.   Nature Communications

Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities

(2020) Lukas Beule et al.   PeerJ

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe

(2020) Leho Tedersoo et al.   Frontiers in Microbiology

Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

(2019) Krista M. Ruppert et al.   Global Ecology and Conservation

Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems

(2019) Paul B. L. George et al.   Nature Communications

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Conventional and organic soil management as divergent drivers of resident and active fractions of major soil food web constituents

(2019) Paula Harkes et al.   Scientific Reports

Bacteria, Fungi and Archaea Domains in Rhizospheric Soil and Their Effects in Enhancing Agricultural Productivity

(2019) Kehinde Odelade et al.   International Journal of Environmental Research and Public Health

Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China

(2019) Cheng-yu Wang et al.   ANNALS OF MICROBIOLOGY

Organic and inorganic fertilizers respectively drive bacterial and fungal community compositions in a fluvo-aquic soil in northern China

(2019) Hong Pan et al.   SOIL & TILLAGE RESEARCH

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Soil quality – A critical review

(2018) Else K. Bünemann et al.   SOIL BIOLOGY & BIOCHEMISTRY

Effects of different management regimes on microbial biodiversity in vineyard soils

(2018) Maximilian Hendgen et al.   Scientific Reports

Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing

(2018) Luhua Yao et al.   PeerJ

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Effect of triple superphosphate and biowaste compost on mycorrhizal colonization and enzymatic P mobilization under maize in a long-term field experiment

(2018) Manuela Peine et al.   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

From vineyard to winery: a source map of microbial diversity driving wine fermentation

(2017) Peter Morrison-Whittle et al.   ENVIRONMENTAL MICROBIOLOGY

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere

(2017) Ubiana C. Silva et al.   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Climate-smart soils

(2016) Keith Paustian et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Soil Degradation, Land Scarcity and Food Security: Reviewing a Complex Challenge

(2016) Tiziano Gomiero   Sustainability

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Quantifying the relative roles of selective and neutral processes in defining eukaryotic microbial communities

(2015) Peter Morrison-Whittle et al.   ISME Journal

A new antibiotic kills pathogens without detectable resistance

(2015) Losee L. Ling et al.   NATURE

Soil biodiversity and DNA barcodes: opportunities and challenges

(2015) Alberto Orgiazzi et al.   SOIL BIOLOGY & BIOCHEMISTRY

Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

(2014) Chenxue Yang et al.   ECOLOGICAL INDICATORS

Distinct soil microbial diversity under long-term organic and conventional farming

(2014) Martin Hartmann et al.   ISME Journal

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

(2013) Tomáš Větrovský et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

An enhanced software tool to support better use of manure nutrients: MANNER-NPK

(2013) F. A. Nicholson et al.   SOIL USE AND MANAGEMENT

Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

(2012) R. Henrik Nilsson et al.   Evolutionary Bioinformatics

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

(2012) Hirokazu Toju et al.   PLoS One

Global food demand and the sustainable intensification of agriculture

(2011) D. Tilman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of recent and accumulated livestock manure carbon additions on soil fertility and quality

(2010) A. Bhogal et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

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

(2010) Johannes Rousk et al.   ISME Journal

Organic carbon additions: effects on soil bio-physical and physico-chemical properties

(2009) A. Bhogal et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Microbial contributions to climate change through carbon cycle feedbacks

(2008) Richard D Bardgett et al.   ISME Journal