Predicting soil farming system and attributes based on soil bacterial community

Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields

(2021) Ademir Durrer et al.   PeerJ

MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks

(2020) Sunil Nagpal et al.   NUCLEIC ACIDS RESEARCH

Using soil bacterial communities to predict physico-chemical variables and soil quality

(2020) Syrie M. Hermans et al.   Microbiome

Soil Microbiomes Under Climate Change and Implications for Carbon Cycling

(2020) Dan Naylor et al.   Annual Review of Environment and Resources

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt

(2020) Jun Yuan et al.   ISME Journal

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems

(2020) Begüm D. Topçuoğlu et al.   mBio

Microbial metabolic efficiency and community stability in high and low fertility soils following wheat residue addition

(2020) Benjuan Liu et al.   APPLIED SOIL ECOLOGY

A novel generalized odd log-logistic Maxwell-based regression with application to microbiology

(2020) Fábio Prataviera et al.   APPLIED MATHEMATICAL MODELLING

Using a soil bacterial species balance index to estimate potato crop productivity

(2019) Thomas Jeanne et al.   PLoS One

Effects of tillage managements and maize straw returning on soil microbiome using 16S rDNA sequencing

(2019) Xinyao Xia et al.   Journal of Integrative Plant Biology

Obscure soil microbes and where to find them

(2019) Manuel Delgado-Baquerizo   ISME Journal

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

(2019) Samiran Banerjee et al.   ISME Journal

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Can bacterial indicators of a grassy woodland restoration inform ecosystem assessment and microbiota-mediated human health?

(2019) Craig Liddicoat et al.   ENVIRONMENT INTERNATIONAL

Soil and the intensification of agriculture for global food security

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

Soil hydrology drives ecological niche differentiation in a native prairie microbiome

(2019) James S Griffin et al.   FEMS MICROBIOLOGY ECOLOGY

Soil microbiomes and climate change

(2019) Janet K. Jansson et al.   NATURE REVIEWS MICROBIOLOGY

Effects of tillage practices on soil microbiome and agricultural parameters

(2019) Judith Kraut-Cohen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Forest-to-agriculture conversion in Amazon drives soil microbial communities and N-cycle

(2019) Luis Fernando Merloti et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities

(2019) Duo Jiang et al.   Frontiers in Genetics

Predatory Myxococcales are widely distributed in and closely correlated with the bacterial community structure of agricultural land

(2019) Wenhui Wang et al.   APPLIED SOIL ECOLOGY

Exploring a world of a thousand dimensions

(2019) Catalina A. Vallejos   NATURE BIOTECHNOLOGY

Trends in Global Agricultural Land Use: Implications for Environmental Health and Food Security

(2018) Navin Ramankutty et al.   Annual Review of Plant Biology

Zero-inflated generalized Dirichlet multinomial regression model for microbiome compositional data analysis

(2018) Zheng-Zheng Tang et al.   BIOSTATISTICS

Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring

(2018) Tristan Cordier et al.   Molecular Ecology Resources

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

Intercropping Acacia mangium stimulates AMF colonization and soil phosphatase activity in Eucalyptus grandis

(2018) Daniel Bini et al.   SCIENTIA AGRICOLA

Geographical and Cultivar Features Differentiate Grape Microbiota in Northern Italy and Spain Vineyards

(2018) Valerio Mezzasalma et al.   Frontiers in Microbiology

A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform

(2018) Monica Pichler et al.   MicrobiologyOpen

Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures

(2018) Daniel R. Lammel et al.   Microbiome

A change of perspective in network centrality

(2018) Carla Sciarra et al.   Scientific Reports

Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community

(2017) Yi Wang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Disentangling Interactions in the Microbiome: A Network Perspective

(2017) Mehdi Layeghifard et al.   TRENDS IN MICROBIOLOGY

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

(2017) Manoeli Lupatini et al.   Frontiers in Microbiology

Maize growth responses to soil microbes and soil properties after fertilization with different green manures

(2016) Jiemeng Tao et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Diversity is the question, not the answer

(2016) Ashley Shade   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability

(2016) S. Franz Bender et al.   TRENDS IN ECOLOGY & EVOLUTION

Microbial diversity drives multifunctionality in terrestrial ecosystems

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

Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling

(2016) Andrew M. Thomas et al.   Frontiers in Cellular and Infection Microbiology

A novel bacterial community index to assess stream ecological health

(2015) Kelvin E. M. Lau et al.   FRESHWATER BIOLOGY

Soil biodiversity and DNA barcodes: opportunities and challenges

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

Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4

(2015) Javier Pascual et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

(2015) Mark B. Smith et al.   mBio

Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon

(2015) Acacio A. Navarrete et al.   Frontiers in Microbiology

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

qgraph: Network Visualizations of Relationships in Psychometric Data

(2015) Sacha Epskamp et al.   Journal of Statistical Software

Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis

(2015) Sébastien Boutin et al.   PLoS One

Köppen's climate classification map for Brazil

(2014) Clayton Alcarde Alvares et al.   METEOROLOGISCHE ZEITSCHRIFT

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

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

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

Soil enzyme activities, microbial communities, and carbon and nitrogen availability in organic agroecosystems across an intensively-managed agricultural landscape

(2013) Timothy M. Bowles et al.   SOIL BIOLOGY & BIOCHEMISTRY

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

Permanganate Oxidizable Carbon Reflects a Processed Soil Fraction that is Sensitive to Management

(2012) Steven W. Culman et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Putting people in the map: anthropogenic biomes of the world

(2007) Erle C Ellis et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT