Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities

(2017) Roland C Wilhelm et al.   ISME Journal

A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting

(2017) Roland C. Wilhelm et al.   Scientific Data

Silvibacterium bohemicum gen. nov. sp. nov., an acidobacterium isolated from coniferous soil in the Bohemian Forest National Park

(2016) Salvador Lladó et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

Identification of Manganese Superoxide Dismutase from Sphingobacterium sp. T2 as a Novel Bacterial Enzyme for Lignin Oxidation

(2015) Goran M. M. Rashid et al.   ACS Chemical Biology

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

Lignin decomposition is sustained under fluctuating redox conditions in humid tropical forest soils

(2015) Steven J. Hall et al.   GLOBAL CHANGE BIOLOGY

Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils

(2015) Hilary T C Leung et al.   ISME Journal

Influence of Hyphal Inoculum potential on the Competitive Success of Fungi Colonizing Wood

(2015) Zewei Song et al.   MICROBIAL ECOLOGY

Two decades of warming increases diversity of a potentially lignolytic bacterial community

(2015) Grace Pold et al.   Frontiers in Microbiology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Feature Selection with theBorutaPackage

(2015) Miron B. Kursa et al.   Journal of Statistical Software

Sensitive, Efficient Quantitation of13C-Enriched Nucleic Acids via Ultrahigh-Performance Liquid Chromatography–Tandem Mass Spectrometry for Applications in Stable Isotope Probing

(2014) Roland Wilhelm et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Potential of Cometabolic Transformation of Polysaccharides and Lignin in Lignocellulose by Soil Actinobacteria

(2014) Tomáš Větrovský et al.   PLoS One

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

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

Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

(2014) Y. Verastegui et al.   mBio

Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels

(2013) Yining Zeng et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Spatial variability of soil fungal and bacterial abundance: Consequences for carbon turnover along a transition from a forested to clear-cut site

(2013) Carolyn Churchland et al.   SOIL BIOLOGY & BIOCHEMISTRY

Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils

(2013) Hannah L. Woo et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Identification and Characterization of a Multifunctional Dye Peroxidase from a Lignin-Reactive Bacterium

(2012) Margaret E. Brown et al.   ACS Chemical Biology

Phylogenetic Distribution of Potential Cellulases in Bacteria

(2012) Renaud Berlemont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing

(2012) Stephanie A. Eichorst et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A trait-based approach for modelling microbial litter decomposition

(2012) S. D. Allison   ECOLOGY LETTERS

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

(2012) Martin Hartmann et al.   ISME Journal

Isolation of bacterial strains able to metabolize lignin from screening of environmental samples

(2012) C.R. Taylor et al.   JOURNAL OF APPLIED MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome analyses highlight the different biological roles of cellulases

(2012) Felix Mba Medie et al.   NATURE REVIEWS MICROBIOLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

How Does Plant Cell Wall Nanoscale Architecture Correlate with Enzymatic Digestibility?

(2012) S.-Y. Ding et al.   SCIENCE

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Towards industrially-feasible delignification and pitch removal by treating paper pulp with Myceliophthora thermophila laccase and a phenolic mediator

(2011) Esteban D. Babot et al.   BIORESOURCE TECHNOLOGY

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

(2011) Kristen M. DeAngelis et al.   PLoS One

Complete genome sequence of “Enterobacter lignolyticus” SCF1

(2011) Kristen M. DeAngelis et al.   Standards in Genomic Sciences

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Considering fungal:bacterial dominance in soils – Methods, controls, and ecosystem implications

(2010) Michael S. Strickland et al.   SOIL BIOLOGY & BIOCHEMISTRY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil

(2009) Larissa B. Folman et al.   FEMS MICROBIOLOGY ECOLOGY