Organic management enhances soil quality and drives microbial community diversity in cocoa production systems

Plant diversity enhanced soil fungal diversity and microbial resistance to plant invasion

(2021) Congcong Shen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity and asynchrony in soil microbial communities stabilizes ecosystem functioning

(2021) Cameron Wagg et al.   eLife

Soil carbon sequestration by agroforestry systems in China: A meta-analysis

(2021) Rico Hübner et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Impact of common sample pre-treatments on key soil microbial properties

(2021) Julia Schroeder et al.   SOIL BIOLOGY & BIOCHEMISTRY

Belowground functioning of agroforestry systems: recent advances and perspectives

(2020) Rémi Cardinael et al.   PLANT AND SOIL

The effect of short-term vs. long-term soil moisture stress on the physiological response of three cocoa (Theobroma cacao L.) cultivars

(2020) Wiebke Niether et al.   PLANT GROWTH REGULATION

How microbes can, and cannot, be used to assess soil health

(2020) Noah Fierer et al.   SOIL BIOLOGY & BIOCHEMISTRY

Responses of Soil Bacterial and Fungal Communities to Organic and Conventional Farming Systems in East China

(2019) Hanlin Zhang et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Recommendations for soil microbiome analyses

(2019) P. Nannipieri et al.   BIOLOGY AND FERTILITY OF SOILS

Soil and the intensification of agriculture for global food security

(2019) Peter M. Kopittke et al.   ENVIRONMENT INTERNATIONAL

Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica

(2019) Emma Martinez-Alonso et al.   Scientific Reports

Crop-diversification and organic management increase the energy efficiency of cacao plantations

(2019) David Pérez-Neira et al.   AGRICULTURAL SYSTEMS

Soil quality and phosphorus status after nine years of organic and conventional farming at two input levels in the Central Highlands of Kenya

(2019) C. von Arb et al.   GEODERMA

Agroforestry for soil health

(2018) Jeanne Dollinger et al.   AGROFORESTRY SYSTEMS

Shade trees and tree pruning alter throughfall and microclimate in cocoa (Theobroma cacao L.) production systems

(2018) Wiebke Niether et al.   ANNALS OF FOREST SCIENCE

CARBON STOCKS, LITTERFALL AND PRUNING RESIDUES IN MONOCULTURE AND AGROFORESTRY CACAO PRODUCTION SYSTEMS

(2018) ULF SCHNEIDEWIND et al.   EXPERIMENTAL AGRICULTURE

Soil quality – A critical review

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

Below- and aboveground production in cocoa monocultures and agroforestry systems

(2018) Wiebke Niether et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Sensitivity of labile carbon fractions to tillage and organic matter management and their potential as comprehensive soil quality indicators across pedoclimatic conditions in Europe

(2018) Giulia Bongiorno et al.   ECOLOGICAL INDICATORS

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

(2017) Chen Qian et al.   JOURNAL OF PROTEOME RESEARCH

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

(2017) Luisa W. Hugerth et al.   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

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

Many shades of gray—The context-dependent performance of organic agriculture

(2017) Verena Seufert et al.   Science Advances

Organic farming enhances soil microbial abundance and activity—A meta-analysis and meta-regression

(2017) Martina Lori et al.   PLoS One

Measuring respiration profiles of soil microbial communities across Europe using MicroResp™ method

(2016) R.E. Creamer et al.   APPLIED SOIL ECOLOGY

Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data

(2016) Gregory B. Gloor et al.   CANADIAN JOURNAL OF MICROBIOLOGY

COCOA AND TOTAL SYSTEM YIELDS OF ORGANIC AND CONVENTIONAL AGROFORESTRY VS. MONOCULTURE SYSTEMS IN A LONG-TERM FIELD TRIAL IN BOLIVIA

(2016) M. SCHNEIDER et al.   EXPERIMENTAL AGRICULTURE

Linking soils to ecosystem services — A global review

(2016) Kabindra Adhikari et al.   GEODERMA

Fungal identification biases in microbiome projects

(2016) Leho Tedersoo et al.   Environmental Microbiology Reports

Microbial diversity drives multifunctionality in terrestrial ecosystems

(2016) Manuel Delgado-Baquerizo et al.   Nature Communications

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

(2016) Jonathan Thorsen et al.   Microbiome

zCompositions — R package for multivariate imputation of left-censored data under a compositional approach

(2015) Javier Palarea-Albaladejo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Determinants of bacterial communities in Canadian agroforestry systems

(2015) Samiran Banerjee et al.   ENVIRONMENTAL MICROBIOLOGY

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Planetary boundaries: Guiding human development on a changing planet

(2015) W. Steffen et al.   SCIENCE

Soil organic carbon sequestration in agroforestry systems. A review

(2014) Klaus Lorenz et al.   Agronomy for Sustainable Development

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

(2014) Martin Hartmann et al.   ISME Journal

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

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

Comparing the yields of organic and conventional agriculture

(2012) Verena Seufert et al.   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Enhanced top soil carbon stocks under organic farming

(2012) A. Gattinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using species combinations in indicator value analyses

(2012) Miquel De Cáceres et al.   Methods in Ecology and Evolution

The genera of Hyphomycetes – 2011 update

(2011) K.A. Seifert et al.   PERSOONIA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics

(2010) Luis Alcaraz et al.   BMC GENOMICS

Taxonomy and phylogeny of the Fusarium dimerum species group

(2009) Hans-Josef Schroers et al.   MYCOLOGIA

TerraGenome: a consortium for the sequencing of a soil metagenome

(2009) Timothy M. Vogel et al.   NATURE REVIEWS MICROBIOLOGY