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

A trait-based understanding of wood decomposition by fungi

(2020) Nicky Lustenhouwer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood

(2020) María Gómez-Brandón et al.   Scientific Reports

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

(2020) Tomáš Větrovský et al.   Scientific Data

Convergence, divergence or chaos? Consequences of tree trunk decay for pedogenesis and the soil microbiome in a temperate natural forest

(2020) P. Šamonil et al.   GEODERMA

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

(2020) Shingo Miyauchi et al.   Nature Communications

Carbon flux from decomposing wood and its dependency on temperature, wood N 2 fixation rate, moisture and fungal composition in a Norway spruce forest

(2019) Katja T. Rinne‐Garmston (Rinne) et al.   GLOBAL CHANGE BIOLOGY

Strategies of carbon and nitrogen acquisition by saprotrophic and ectomycorrhizal fungi in Finnish boreal Picea abies-dominated forests

(2019) J. Chen et al.   Fungal Biology

Climatic controls of decomposition drive the global biogeography of forest-tree symbioses

(2019) B. S. Steidinger et al.   NATURE

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

Substrate stoichiometry determines nitrogen fixation throughout succession in southern Chinese forests

(2019) Mianhai Zheng et al.   ECOLOGY LETTERS

Bacterial communities of decaying Norway spruce follow distinct slope exposure and time-dependent trajectories

(2018) M Probst et al.   ENVIRONMENTAL MICROBIOLOGY

Methanotrophs are core members of the diazotroph community in decaying Norway spruce logs

(2018) Raisa Mäkipää et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fungus wars: basidiomycete battles in wood decay

(2018) J. Hiscox et al.   STUDIES IN MYCOLOGY

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States

(2018) Rachel Mackelprang et al.   Frontiers in Microbiology

Wood decay rates of 13 temperate tree species in relation to wood properties, enzyme activities and organismic diversities

(2017) Tiemo Kahl et al.   FOREST ECOLOGY AND MANAGEMENT

dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation

(2017) Le Huang et al.   NUCLEIC ACIDS RESEARCH

Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments

(2017) Anja Worrich et al.   Nature Communications

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

(2017) Lucia Žifčáková et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Accumulation rates and sources of external nitrogen in decaying wood in a Norway spruce dominated forest

(2016) Katja T. Rinne et al.   FUNCTIONAL ECOLOGY

Fungi associated with decomposing deadwood in a natural beech-dominated forest

(2016) Petr Baldrian et al.   Fungal Ecology

Patterns of carbon, nitrogen and phosphorus dynamics in decomposing wood blocks in Canadian forests

(2016) C. E. Smyth et al.   PLANT AND SOIL

Global biogeography of microbial nitrogen-cycling traits in soil

(2016) Michaeline B. Nelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Dinghua Li et al.   BIOINFORMATICS

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

(2015) Lucia Žifčáková et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Mapping tree density at a global scale

(2015) T. W. Crowther et al.   NATURE

Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water

(2015) Mikkel Bentzon-Tilia et al.   mBio

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

(2015) Cedar N. Hesse 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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change

(2014) Kristina J. Anderson-Teixeira et al.   GLOBAL CHANGE BIOLOGY

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus

(2014) Emmanuel Prestat et al.   NUCLEIC ACIDS RESEARCH

Network Analysis Reveals Ecological Links between N-Fixing Bacteria and Wood-Decaying Fungi

(2014) Björn Hoppe et al.   PLoS One

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Nitrogen fixation and methanotrophy in forest mosses along a N deposition gradient

(2013) Sanna M. Leppänen et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Crossdating of disturbances by tree uprooting: Can treethrow microtopography persist for 6000years?

(2013) P. Šamonil et al.   FOREST ECOLOGY AND MANAGEMENT

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Patterns of new versus recycled primary production in the terrestrial biosphere

(2013) C. C. Cleveland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) J Gregory Caporaso et al.   ISME Journal

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

Evidence for methane production by saprotrophic fungi

(2012) Katharina Lenhart et al.   Nature Communications

Interactions of temperature and moisture with respiration from coarse woody debris in experimental forest canopy gaps

(2011) Jodi A. Forrester et al.   FOREST ECOLOGY AND MANAGEMENT

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

A Large and Persistent Carbon Sink in the World's Forests

(2011) Y. Pan et al.   SCIENCE

The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

(2011) D. C. Eastwood et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Assembly history dictates ecosystem functioning: evidence from wood decomposer communities

(2010) Tadashi Fukami et al.   ECOLOGY LETTERS

Local variability of stand structural features in beech dominated natural forests of Central Europe: Implications for sampling

(2010) Kamil Král et al.   FOREST ECOLOGY AND MANAGEMENT

Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in decaying wood

(2009) Vendula Valášková et al.   ISME Journal

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Global meta-analysis of wood decomposition rates: a role for trait variation among tree species?

(2008) James T. Weedon et al.   ECOLOGY LETTERS

A unifying framework for dinitrogen fixation in the terrestrial biosphere

(2008) Benjamin Z. Houlton et al.   NATURE

Old-growth forests as global carbon sinks

(2008) Sebastiaan Luyssaert et al.   NATURE