Specific utilization of biopolymers of plant and fungal origin reveals the existence of substrate-specific guilds for bacteria in temperate forest soils

Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition

(2021) Vojtěch Tláskal et al.   mSystems

Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood

(2021) S. Mieszkin et al.   SOIL BIOLOGY & BIOCHEMISTRY

Long-term decomposition of litter in the montane forest and the definition of fungal traits in the successional space

(2020) Martina Štursová et al.   Fungal Ecology

Feeding on fungi: Genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass

(2020) Robert Starke et al.   ENVIRONMENTAL MICROBIOLOGY

Bioconversion of chitin and concomitant production of chitinase and N-acetylglucosamine by novel Achromobacter xylosoxidans isolated from shrimp waste disposal area

(2020) Kumaran Subramanian et al.   Scientific Reports

Litter-inhabiting fungi show high level of specialization towards biopolymers composing plant and fungal biomass

(2020) Camelia Algora Gallardo et al.   BIOLOGY AND FERTILITY OF SOILS

Metagenomics and stable isotope probing reveal the complementary contribution of fungal and bacterial communities in the recycling of dead biomass in forest soil

(2020) Rubén López-Mondéjar et al.   SOIL BIOLOGY & BIOCHEMISTRY

Enhanced konjac glucomannan hydrolysis by lytic polysaccharide monooxygenases and generating prebiotic oligosaccharides

(2020) Fei Li et al.   CARBOHYDRATE POLYMERS

The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans

(2019) Sabina Leanti La Rosa et al.   Nature Communications

Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes

(2019) Rubén López-Mondéjar et al.   BIOTECHNOLOGY ADVANCES

Ecological Functions of Agricultural Soil Bacteria and Microeukaryotes in Chitin Degradation: A Case Study

(2019) Adam S. Wieczorek et al.   Frontiers in Microbiology

Tracking of the activity of individual bacteria in temperate forest soils shows guild-specific responses to seasonality

(2019) Salvador Lladó et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi

(2019) Amy E. Zanne et al.   BIOLOGICAL REVIEWS

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses

(2018) Tomáš Větrovský et al.   BIOINFORMATICS

Litter chemistry influences decomposition through activity of specific microbial functional guilds

(2018) Jennifer M. Bhatnagar et al.   ECOLOGICAL MONOGRAPHS

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling

(2018) Ruben López-Mondéjar et al.   ISME Journal

Nutrient content affects the turnover of fungal biomass in forest topsoil and the composition of associated microbial communities

(2018) Vendula Brabcová et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

(2018) Roland C. Wilhelm et al.   ISME Journal

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism

(2017) Naofumi Kamimura et al.   Environmental Microbiology Reports

Feed in summer, rest in winter: microbial carbon utilization in forest topsoil

(2017) Lucia Žifčáková et al.   Microbiome

Decoding the complete arsenal for cellulose and hemicellulose deconstruction in the highly efficient cellulose decomposer Paenibacillus O199

(2016) Rubén López-Mondéjar et al.   Biotechnology for Biofuels

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

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

Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community

(2016) Vendula Brabcová et al.   NEW PHYTOLOGIST

Degradation of lignin β-aryl ether units in Arabidopsis thaliana expressing LigD , LigF and LigG from Sphingomonas paucimobilis SYK-6

(2016) Ewelina Mnich et al.   PLANT BIOTECHNOLOGY JOURNAL

The decadal state of the terrestrial carbon cycle: Global retrievals of terrestrial carbon allocation, pools, and residence times

(2016) A. Anthony Bloom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Glycoside Hydrolases across Environmental Microbial Communities

(2016) Renaud Berlemont et al.   PLoS Computational Biology

Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil

(2016) Susanne Kramer et al.   Frontiers in 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

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems

(2016) Rubén López-Mondéjar et al.   Scientific Reports

Influence of tree shape and evolutionary time-scale on phylogenetic diversity metrics

(2015) Florent Mazel et al.   ECOGRAPHY

Revisiting the hypothesis that fungal-to-bacterial dominance characterizes turnover of soil organic matter and nutrients

(2015) Johannes Rousk et al.   ECOLOGICAL MONOGRAPHS

Microbial ecosystems are dominated by specialist taxa

(2015) Mahendra Mariadassou et al.   ECOLOGY LETTERS

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter

(2015) Lucia Žifčáková et al.   ENVIRONMENTAL MICROBIOLOGY

Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi

(2015) Ivana Eichlerová et al.   Fungal Ecology

Quantitative assessment of the differential impacts of arbuscular and ectomycorrhiza on soil carbon cycling

(2015) Nadejda A. Soudzilovskaia et al.   NEW PHYTOLOGIST

Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees

(2015) Michaela Urbanová et al.   SOIL BIOLOGY & BIOCHEMISTRY

Genomic Potential for Polysaccharide Deconstruction in Bacteria

(2014) Renaud Berlemont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial communities in chitin-amended soil as revealed by 16S rRNA gene based pyrosequencing

(2014) Mariana Silvia Cretoiu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

(2013) Amy E Zimmerman et al.   ISME Journal

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Seasonal dynamics of fungal communities in a temperate oak forest soil

(2013) Jana Voříšková et al.   NEW PHYTOLOGIST

The production and turnover of extramatrical mycelium of ectomycorrhizal fungi in forest soils: role in carbon cycling

(2013) A. Ekblad et al.   PLANT AND SOIL

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

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

Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers

(2012) Martina Štursová et al.   FEMS MICROBIOLOGY ECOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Fungal community on decomposing leaf litter undergoes rapid successional changes

(2012) Jana Voříšková et al.   ISME Journal

Responses of the extracellular enzyme activities in hardwood forest to soil temperature and seasonality and the potential effects of climate change

(2012) Petr Baldrian et al.   SOIL BIOLOGY & BIOCHEMISTRY

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian et al.   ISME Journal

Validation and Application of a PCR Primer Set to Quantify Fungal Communities in the Soil Environment by Real-Time Quantitative PCR

(2011) Nicolas Chemidlin Prévost-Bouré et al.   PLoS One

Picante: R tools for integrating phylogenies and ecology

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Small-scale distribution of extracellular enzymes, fungal, and bacterial biomass in Quercus petraea forest topsoil

(2010) Petr Baldrian et al.   BIOLOGY AND FERTILITY OF SOILS

Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition

(2010) Jaroslav Šnajdr et al.   FEMS MICROBIOLOGY ECOLOGY

Metabolic responses of novel cellulolytic and saccharolytic agricultural soil Bacteria to oxygen

(2009) Stefanie Schellenberger et al.   ENVIRONMENTAL MICROBIOLOGY

Old-growth forests as global carbon sinks

(2008) Sebastiaan Luyssaert et al.   NATURE

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Spatial variability of enzyme activities and microbial biomass in the upper layers of Quercus petraea forest soil

(2008) Jaroslav Šnajdr et al.   SOIL BIOLOGY & BIOCHEMISTRY