A critical perspective on interpreting amplicon sequencing data in soil ecological research

Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data

(2021) Shilei Wang et al.   mSystems

High-throughput sequencing view on the magnitude of global fungal diversity

(2021) Petr Baldrian et al.   FUNGAL DIVERSITY

Quantifying short-range variation of soil texture and total carbon of a 330-ha farm

(2021) Yakun Zhang et al.   CATENA

Open challenges for microbial network construction and analysis

(2021) Karoline Faust   ISME Journal

Network analysis and subsequent culturing reveal keystone taxa involved in microbial litter decomposition dynamics

(2021) Haiping Zheng et al.   SOIL BIOLOGY & BIOCHEMISTRY

Next-generation physiology approaches to study microbiome function at single cell level

(2020) Roland Hatzenpichler et al.   NATURE REVIEWS MICROBIOLOGY

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

(2020) Paul Carini et al.   mBio

Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes

(2020) Samuel Bickel et al.   Nature Communications

Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations

(2020) Kasia Piwosz et al.   mSphere

Co‐occurrence is not evidence of ecological interactions

(2020) F. Guillaume Blanchet et al.   ECOLOGY LETTERS

Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves

(2020) Julian Regalado et al.   ISME Journal

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

The ecology of heterogeneity: soil bacterial communities and C dynamics

(2020) Naoise Nunan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Low Turnover of Soil Bacterial rRNA at Low Temperatures

(2020) Morten Dencker Schostag et al.   Frontiers in Microbiology

A Primer for Microbiome Time-Series Analysis

(2020) Ashley R. Coenen et al.   Frontiers in Genetics

Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale

(2020) Kaoping Zhang et al.   mSystems

Experimental testing of hypotheses for temperature- and pH-based niche specialisation of ammonia oxidising archaea and bacteria

(2020) A. Aigle et al.   ENVIRONMENTAL MICROBIOLOGY

Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought

(2020) Joana Séneca et al.   ISME Journal

Rusty sink of rhizodeposits and associated keystone microbiomes

(2020) Peduruhewa H. Jeewani et al.   SOIL BIOLOGY & BIOCHEMISTRY

Towards meaningful scales in ecosystem microbiome research

(2020) Francisco Dini‐Andreote et al.   ENVIRONMENTAL MICROBIOLOGY

Cutting out the middle clam: lucinid endosymbiotic bacteria are also associated with seagrass roots worldwide

(2020) Belinda C. Martin et al.   ISME Journal

Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment

(2020) Nicholas J. Reichart et al.   ISME Journal

16S rRNA Gene Copy Number Normalization Does Not Provide More Reliable Conclusions in Metataxonomic Surveys

(2020) Robert Starke et al.   MICROBIAL ECOLOGY

Alpha-, beta-, and gamma-diversity of bacteria varies across habitats

(2020) Kendra E. Walters et al.   PLoS One

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

Strong priming of soil organic matter induced by frequent input of labile carbon

(2020) Jie Zhou et al.   SOIL BIOLOGY & BIOCHEMISTRY

D2O-Isotope-Labeling Approach to Probing Phosphate-Solubilizing Bacteria in Complex Soil Communities by Single-Cell Raman Spectroscopy

(2019) Hong-Zhe Li et al.   ANALYTICAL CHEMISTRY

Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities

(2019) Yangyang Jia et al.   mSystems

An automated Raman-based platform for the sorting of live cells by functional properties

(2019) Kang Soo Lee et al.   Nature Microbiology

Scientists rise up against statistical significance

(2019) Valentin Amrhein et al.   NATURE

Moving to a World Beyond “p 

(2019) Ronald L. Wasserstein et al.   AMERICAN STATISTICIAN

Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales

(2019) Regina L. Wilpiszeski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Predictive genomic traits for bacterial growth in culture versus actual growth in soil

(2019) Junhui Li et al.   ISME Journal

Towards PacBio‐based pan‐eukaryote metabarcoding using full‐length ITS sequences

(2019) Leho Tedersoo et al.   Environmental Microbiology Reports

Probing the active fraction of soil microbiomes using BONCAT-FACS

(2019) Estelle Couradeau et al.   Nature Communications

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms

(2019) Michael Lukumbuzya et al.   Frontiers in Microbiology

High proportions of bacteria and archaea across most biomes remain uncultured

(2019) Andrew D. Steen et al.   ISME Journal

Generating amplicon reads for microbial community assessment with next‐generation sequencing

(2019) M. Gołębiewski et al.   JOURNAL OF APPLIED MICROBIOLOGY

Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes

(2019) Marta Goberna et al.   Molecular Ecology Resources

Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity

(2019) Qing Zheng et al.   SOIL BIOLOGY & BIOCHEMISTRY

Consistent and correctable bias in metagenomic sequencing experiments

(2019) Michael R McLaren et al.   eLife

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands

(2019) Selma Vieira et al.   ISME Journal

A meta-analysis of global fungal distribution reveals climate-driven patterns

(2019) Tomáš Větrovský et al.   Nature Communications

A Bioinformatics Guide to Plant Microbiome Analysis

(2019) Rares Lucaciu et al.   Frontiers in Plant Science

Optimization of a Method To Quantify Soil Bacterial Abundance by Flow Cytometry

(2019) Banafshe Khalili et al.   mSphere

Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils

(2019) Qing-Lin Chen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

How, When, and Where Relic DNA Affects Microbial Diversity

(2018) J. T. Lennon et al.   mBio

Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP – A Bioinformatics Pipeline for Analyzing nifH Amplicon Data

(2018) Roey Angel et al.   Frontiers in Microbiology

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

Absolute quantitation of microbiota abundance in environmental samples

(2018) Andrzej Tkacz et al.   Microbiome

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

(2018) Simon A. Hardwick et al.   Nature Communications

Soil bacterial networks are less stable under drought than fungal networks

(2018) Franciska T. de Vries et al.   Nature Communications

Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity

(2018) Andrew Dopheide et al.   Methods in Ecology and Evolution

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

(2018) Philippe C. Baveye et al.   Frontiers in Microbiology

Mycobiome diversity: high-throughput sequencing and identification of fungi

(2018) R. Henrik Nilsson et al.   NATURE REVIEWS MICROBIOLOGY

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

(2017) Benjamin J Callahan et al.   ISME Journal

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Using null models to infer microbial co-occurrence networks

(2017) Nora Connor et al.   PLoS One

A phylogenetic transform enhances analysis of compositional microbiota data

(2017) Justin D Silverman et al.   eLife

Resolving Species Level Changes in a Representative Soil Bacterial Community Using Microfluidic Quantitative PCR

(2017) Hannah Kleyer 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

Balance Trees Reveal Microbial Niche Differentiation

(2017) James T. Morton et al.   mSystems

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Single cell stable isotope probing in microbiology using Raman microspectroscopy

(2016) Yun Wang et al.   CURRENT OPINION IN BIOTECHNOLOGY

Tracking microbial interactions with NanoSIMS

(2016) Niculina Musat et al.   CURRENT OPINION IN BIOTECHNOLOGY

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

Strategies to improve reference databases for soil microbiomes

(2016) Jinlyung Choi et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Microbial carbon use efficiency and biomass turnover times depending on soil depth – Implications for carbon cycling

(2016) Marie Spohn et al.   SOIL BIOLOGY & BIOCHEMISTRY

Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge

(2016) Aline Frossard et al.   Frontiers in Microbiology

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

(2016) Frank Stämmler et al.   Microbiome

Quantitative Microbial Ecology through Stable Isotope Probing

(2015) Bruce A. Hungate et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

(2015) Brendan J. Kelly et al.   BIOINFORMATICS

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Scientific method: Statistical errors

(2014) Regina Nuzzo   NATURE

Root exudation of phytosiderophores from soil-grown wheat

(2014) Eva Oburger et al.   NEW PHYTOLOGIST

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Power analysis for generalized linear mixed models in ecology and evolution

(2014) Paul C. D. Johnson et al.   Methods in Ecology and Evolution

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

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

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

(2014) Florent E Angly et al.   Microbiome

Elucidating the microbial resuscitation cascade in biological soil crusts following a simulated rain event

(2013) Roey Angel et al.   ENVIRONMENTAL MICROBIOLOGY

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Recovery of soil unicellular eukaryotes: An efficiency and activity analysis on the single cell level

(2013) Guillaume Lentendu et al.   JOURNAL OF MICROBIOLOGICAL 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

Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

(2013) Jun Gong et al.   PROTIST

High throughput phospholipid fatty acid analysis of soils

(2012) Jeffrey S. Buyer et al.   APPLIED SOIL ECOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

PCR inhibitors - occurrence, properties and removal

(2012) C. Schrader et al.   JOURNAL OF APPLIED MICROBIOLOGY

Environmental and stoichiometric controls on microbial carbon-use efficiency in soils

(2012) Stefano Manzoni et al.   NEW PHYTOLOGIST

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

The generation and maintenance of diversity in microbial communities

(2011) Noah Fierer et al.   AMERICAN JOURNAL OF BOTANY

Validation of Heavy-Water Stable Isotope Probing for the Characterization of Rapidly Responding Soil Bacteria

(2011) Zachary T. Aanderud et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Phylogeny of nodulation and nitrogen-fixation genes in Bradyrhizobium: supporting evidence for the theory of monophyletic origin, and spread and maintenance by both horizontal and vertical transfer

(2011) P. Menna et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure

(2011) Sébastien Terrat et al.   Microbial Biotechnology

Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2

(2010) B. Drigo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Use and misuse of PLFA measurements in soils

(2010) Åsa Frostegård et al.   SOIL BIOLOGY & BIOCHEMISTRY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH) Improves Signal Intensity and Increases rRNA Accessibility

(2009) K. Stoecker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Rhizosphere: biophysics, biogeochemistry and ecological relevance

(2009) Philippe Hinsinger et al.   PLANT AND SOIL

Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH)

(2008) Thilo Eickhorst et al.   SOIL BIOLOGY & BIOCHEMISTRY

Quantitative assessment of the fungal contribution to microbial tissue in soil

(2008) R JOERGENSEN et al.   SOIL BIOLOGY & BIOCHEMISTRY