Catching change in microbial diversity indicators under different soil organic matter managements: Higher taxonomic resolution, better discrimination?

Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes

(2021) Felipe Bastida et al.   ISME Journal

Transferring concepts from plant to microbial ecology: A framework proposal to identify relevant bacterial functional traits

(2021) Nicolas Romillac et al.   SOIL BIOLOGY & BIOCHEMISTRY

Higher taxa are sufficient to represent biodiversity patterns

(2020) Sandro Souza de Oliveira et al.   ECOLOGICAL INDICATORS

Monitoring soil microbial communities using molecular tools: DNA extraction methods may offset long-term management effects

(2020) F. Changey et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

(2019) Lucie Zinger et al.   MOLECULAR ECOLOGY

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

(2019) Ashish A. Malik et al.   ISME Journal

Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

(2019) Cameron Wagg et al.   Nature Communications

LPSN – List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on

(2018) Aidan C. Parte   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A comparison of the ability of PLFA and 16S rRNA gene metabarcoding to resolve soil community change and predict ecosystem functions

(2018) K.H. Orwin et al.   SOIL BIOLOGY & BIOCHEMISTRY

Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques—validity and compatibility in ecological studies

(2018) Stafva Lindström et al.   PeerJ

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool

(2018) Jo De Vrieze et al.   Microbiome

Soil organic carbon storage as a key function of soils - A review of drivers and indicators at various scales

(2018) Martin Wiesmeier et al.   GEODERMA

Elevational patterns and hierarchical determinants of biodiversity across microbial taxonomic scales

(2018) Chih-Fu Yeh et al.   MOLECULAR ECOLOGY

Unravelling the drivers of aquatic communities using disparate organismal groups and different taxonomic levels

(2016) Annika Vilmi et al.   ECOLOGICAL INDICATORS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Analysing the effect of soil organic matter on bacterial communities using T-RFLP fingerprinting: different methods, different stories?

(2015) A. Blaud et al.   BIOLOGY AND FERTILITY OF SOILS

Bacterial Targets as Potential Indicators of Diesel Fuel Toxicity in Subantarctic Soils

(2014) Josie van Dorst et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment

(2014) Kateryna Zhalnina et al.   MICROBIAL ECOLOGY

Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor

(2014) O.F. Elsayed et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses

(2014) Fabio Stagnari et al.   Frontiers in Microbiology

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

Effects of land utilization patterns on soil microbial communities in an acid red soil based on DNA and PLFA analyses

(2013) Jiao-Yan Ying et al.   JOURNAL OF SOILS AND SEDIMENTS

Four Swedish long-term field experiments with sewage sludge reveal a limited effect on soil microbes and on metal uptake by crops

(2013) Gunnar Börjesson et al.   JOURNAL OF SOILS AND SEDIMENTS

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

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

Soil enzymology: classical and molecular approaches

(2012) P. Nannipieri et al.   BIOLOGY AND FERTILITY OF SOILS

Structure, fluctuation and magnitude of a natural grassland soil metagenome

(2012) Tom O Delmont et al.   ISME Journal

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Effect of Biocontrol Agent Pseudomonas fluorescens 2P24 on Soil Fungal Community in Cucumber Rhizosphere Using T-RFLP and DGGE

(2012) Guanpeng Gao et al.   PLoS One

Sensitivity of soil microbial catabolic profiles to a gradient of carbon inputs: Does the soil organic matter matter?

(2012) T.Z. Lerch et al.   SOIL BIOLOGY & BIOCHEMISTRY

Toward conceptual clarity: PLFA in warmed soils

(2012) Devin L. Wixon et al.   SOIL BIOLOGY & BIOCHEMISTRY

Assessment of the spatial distribution of soil microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using combined PLFA and DGGE analyses

(2011) Eric A. Ben-David et al.   FEMS MICROBIOLOGY ECOLOGY

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Use and misuse of PLFA measurements in soils

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Selecting biological indicators for monitoring soils: A framework for balancing scientific and technical opinion to assist policy development

(2009) Karl Ritz et al.   ECOLOGICAL INDICATORS

Ageing processes and soil microbial community effects on the biodegradation of soil 13C-2,4-D nonextractable residues

(2009) T.Z. Lerch et al.   ENVIRONMENTAL POLLUTION

Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment

(2009) Sara Hallin et al.   ISME Journal

Predictors of gross N mineralization and immobilization during decomposition of stabilized organic matter in agricultural soil

(2008) A. M. Herrmann et al.   EUROPEAN JOURNAL OF SOIL SCIENCE