Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling

SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells

(2019) Parysatis Sachs et al.   Nature Communications

Quantitative assessment of microbial necromass contribution to soil organic matter

(2019) Chao Liang et al.   GLOBAL CHANGE BIOLOGY

High proportions of bacteria and archaea across most biomes remain uncultured

(2019) Andrew D. Steen et al.   ISME Journal

Soil characteristics and land-use drive bacterial community assembly patterns

(2019) Samuel E Barnett et al.   FEMS MICROBIOLOGY ECOLOGY

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

(2018) Nicholas D. Youngblut et al.   PLoS One

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

(2018) Nicholas D. Youngblut et al.   Frontiers in Microbiology

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

(2018) Karen G. Lloyd et al.   mSystems

Viruses in soil: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions

(2018) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models

(2017) William R. Wieder et al.   GLOBAL CHANGE BIOLOGY

Defining the functional traits that drive bacterial decomposer community productivity

(2017) Rachael Evans et al.   ISME Journal

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Phylogenetic conservation of substrate use specialization in leaf litter bacteria

(2017) Kristin L. Dolan et al.   PLoS One

Microbiome Datasets Are Compositional: And This Is Not Optional

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

Strategies to improve reference databases for soil microbiomes

(2016) Jinlyung Choi et al.   ISME Journal

The landscape of microbial phenotypic traits and associated genes

(2016) Maria Brbić et al.   NUCLEIC ACIDS RESEARCH

Managing uncertainty in soil carbon feedbacks to climate change

(2016) Mark A. Bradford et al.   Nature Climate Change

Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

(2016) Charles Pepe-Ranney et al.   Frontiers in Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Soil health and carbon management

(2016) Rattan Lal   Food and Energy Security

Quantitative Microbial Ecology through Stable Isotope Probing

(2015) Bruce A. Hungate et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Explicitly representing soil microbial processes in Earth system models

(2015) William R. Wieder et al.   GLOBAL BIOGEOCHEMICAL CYCLES

The physiology and ecological implications of efficient growth

(2015) Benjamin RK Roller et al.   ISME Journal

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Predictability of the terrestrial carbon cycle

(2014) Yiqi Luo et al.   GLOBAL CHANGE BIOLOGY

Intra-genomic variation in G + C content and its implications for DNA stable isotope probing

(2014) Nicholas D. Youngblut et al.   Environmental Microbiology Reports

Microbe-driven turnover offsets mineral-mediated storage of soil carbon under elevated CO2

(2014) Benjamin N. Sulman et al.   Nature Climate Change

Global soil carbon: understanding and managing the largest terrestrial carbon pool

(2014) Jörn PW Scharlemann et al.   Carbon Management

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation

(2013) Stéphane Dray et al.   ECOLOGY

Effect of Anthropogenic Land-Use and Land-Cover Changes on Climate and Land Carbon Storage in CMIP5 Projections for the Twenty-First Century

(2013) V. Brovkin et al.   JOURNAL OF CLIMATE

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

(2013) Sean T. Berthrong et al.   MICROBIAL ECOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Global soil carbon projections are improved by modelling microbial processes

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

Development of microbial-enzyme-mediated decomposition model parameters through steady-state and dynamic analyses

(2012) Gangsheng Wang et al.   ECOLOGICAL APPLICATIONS

Mapping the niche space of soil microorganisms using taxonomy and traits

(2012) Jay T. Lennon et al.   ECOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Environmental and stoichiometric controls on microbial carbon-use efficiency in soils

(2012) Stefano Manzoni et al.   NEW PHYTOLOGIST

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups

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

Cultivation of unculturable soil bacteria

(2012) Van H.T. Pham et al.   TRENDS IN BIOTECHNOLOGY

Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies

(2012) Adrian Ho et al.   Environmental Microbiology Reports

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Microbial control over carbon cycling in soil

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

Microbial Extracellular Enzymes and the Marine Carbon Cycle

(2010) Carol Arnosti   Annual Review of Marine Science

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Detection of gene pathways with predictive power for breast cancer prognosis

(2010) Shuangge Ma et al.   BMC BIOINFORMATICS

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

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

Molecular-Level Interactions in Soils and Sediments: The Role of Aromatic π-Systems

(2009) Marco Keiluweit et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Cultivating the uncultured: limits, advances and future challenges

(2009) Karine Alain et al.   EXTREMOPHILES

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interactions of Hydrophobic Fractions of Dissolved Organic Matter with Fe3+- and Cu2+-Montmorillonite

(2008) Tamara Polubesova et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Terrestrial ecosystem carbon dynamics and climate feedbacks

(2008) Martin Heimann et al.   NATURE

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY