Microbial interkingdom associations across soil depths reveal network connectivity and keystone taxa linked to soil fine-fraction carbon content

Microorganisms and nutrient stoichiometry as mediators of soil organic matter dynamics

(2020) Elizabeth C. Coonan et al.   NUTRIENT CYCLING IN AGROECOSYSTEMS

Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

(2019) Tess E. Brewer et al.   mBio

Distribution of prokaryotic communities throughout the Chernozem profiles under different land uses for over a century

(2018) Mikhail V. Semenov et al.   APPLIED SOIL ECOLOGY

Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?

(2018) Mara A. Freilich et al.   ECOLOGY

Field study reveals core plant microbiota and relative importance of their drivers

(2018) Kelly Hamonts et al.   ENVIRONMENTAL MICROBIOLOGY

Keystone taxa predict compositional change in microbial communities

(2018) Cristina M. Herren et al.   ENVIRONMENTAL MICROBIOLOGY

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores

(2018) Binu Mani Tripathi et al.   Scientific Reports

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

(2018) Shuo Jiao et al.   Microbiome

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau

(2016) Haiyan Chu et al.   ENVIRONMENTAL MICROBIOLOGY

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

(2016) Bin Ma et al.   ISME Journal

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil

(2016) Samiran Banerjee et al.   SOIL BIOLOGY & BIOCHEMISTRY

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

(2016) Cynthia M. Kallenbach et al.   Nature Communications

Microbial diversity drives multifunctionality in terrestrial ecosystems

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

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

(2016) Andrew Bissett et al.   GigaScience

Inorganic Nutrients Increase Humification Efficiency and C-Sequestration in an Annually Cropped Soil

(2016) Clive A. Kirkby et al.   PLoS One

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

Impact of plant domestication on rhizosphere microbiome assembly and functions

(2015) Juan E. Pérez-Jaramillo et al.   PLANT MOLECULAR BIOLOGY

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

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

(2014) David Berry et al.   Frontiers in Microbiology

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

Temporal variation in surface and subsoil abundance and function of the soil microbial community in an arable soil

(2013) Susanne Kramer et al.   SOIL BIOLOGY & BIOCHEMISTRY

Global soil carbon projections are improved by modelling microbial processes

(2013) William R. Wieder et al.   Nature Climate Change

minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers

(2012) Davide Albanese et al.   BIOINFORMATICS

Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes

(2012) Kelly S. Ramirez et al.   GLOBAL CHANGE BIOLOGY

Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil

(2012) Kathryn G. Eilers et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial control over carbon cycling in soil

(2012) Joshua P. Schimel et al.   Frontiers in Microbiology

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Stable soil organic matter: A comparison of C:N:P:S ratios in Australian and other world soils

(2011) C.A. Kirkby et al.   GEODERMA

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

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

(2011) Albert Barberán et al.   ISME Journal

Persistence of soil organic matter as an ecosystem property

(2011) Michael W. I. Schmidt et al.   NATURE

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes

(2010) C. Will et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Microbial production of recalcitrant organic matter in global soils: implications for productivity and climate policy

(2010) Chao Liang et al.   NATURE REVIEWS MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands

(2009) Martin Hartmann et al.   ENVIRONMENTAL MICROBIOLOGY

Changes in Bacterial and Archaeal Community Structure and Functional Diversity along a Geochemically Variable Soil Profile

(2008) C. M. Hansel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE