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

Loss of deep roots limits biogenic agents of soil development that are only partially restored by decades of forest regeneration

(2018) Sharon A. Billings et al.   Elementa-Science of the Anthropocene

Atmosphere–soil carbon transfer as a function of soil depth

(2018) Jérôme Balesdent et al.   NATURE

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

(2018) Karen G. Lloyd et al.   mSystems

Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils

(2017) Alexandra Schwarz et al.   MICROBIAL ECOLOGY

Atmospheric trace gases support primary production in Antarctic desert surface soil

(2017) Mukan Ji et al.   NATURE

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

(2017) Stephanie Turner et al.   Frontiers in Microbiology

Drivers and patterns of iron redox cycling from surface to bedrock in a deep tropical forest soil: a new conceptual model

(2016) Steven J. Hall et al.   BIOGEOCHEMISTRY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2016) Andrew Bissett et al.   GigaScience

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

(2016) Paul Carini et al.   Nature Microbiology

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Microbiology

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

(2015) Jonathan W. Leff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil

(2015) Natasha C. Banning et al.   Scientific Reports

Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska

(2014) Hye Min Kim et al.   FEMS MICROBIOLOGY ECOLOGY

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest

(2014) Neslihan Taş et al.   ISME Journal

Changes in extracellular enzyme activity and microbial community structure with soil depth at the Luquillo Critical Zone Observatory

(2014) M.M. Stone et al.   SOIL BIOLOGY & BIOCHEMISTRY

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

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

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

Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site

(2011) Xueju Lin et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

(2011) Noah Fierer et al.   ISME Journal

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

Functional microbial community response to nutrient pulses by artificial groundwater recharge practice in surface soils and subsoils

(2010) Kirsten Schütz et al.   FEMS MICROBIOLOGY ECOLOGY

Strategies for culture of ‘unculturable’ bacteria

(2010) Sonia R. Vartoukian et al.   FEMS MICROBIOLOGY LETTERS

Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria

(2010) S. Yabe et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

Effects of carbon additions on iron reduction and phosphorus availability in a humid tropical forest soil

(2009) Daniel Liptzin et al.   SOIL BIOLOGY & BIOCHEMISTRY

Rhizogenic Fe–C redox cycling: a hypothetical biogeochemical mechanism that drives crustal weathering in upland soils

(2008) Ryan L. Fimmen et al.   BIOGEOCHEMISTRY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Soil organic matter in soil depth profiles: Distinct carbon preferences of microbial groups during carbon transformation

(2007) Christiane Kramer et al.   SOIL BIOLOGY & BIOCHEMISTRY