Niche differentiation of bacteria and fungi in carbon and nitrogen cycling of different habitats in a temperate coniferous forest: A metaproteomic approach

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

High proportions of bacteria are culturable across major biomes

(2019) Adam C. Martiny   ISME Journal

Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities

(2019) Manuel Kleiner   mSystems

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

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

Associations of Circulating Protein Levels With Lipid Fractions in the General Population

(2018) Sylwia M. Figarska et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA

(2018) Katerina Papp et al.   ISME Journal

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage through two-dimensional liquid chromatography

(2018) Stephen J. Callister et al.   SOIL BIOLOGY & BIOCHEMISTRY

Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics

(2018) Robert Starke et al.   Journal of Proteomics

Challenges and perspectives of metaproteomic data analysis

(2017) Robert Heyer et al.   JOURNAL OF BIOTECHNOLOGY

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

(2017) Salvador Lladó et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

(2017) Le Huang et al.   NUCLEIC ACIDS RESEARCH

Advances in the application of amino acid nitrogen isotopic analysis in ecological and biogeochemical studies

(2017) Naohiko Ohkouchi et al.   ORGANIC GEOCHEMISTRY

Unpacking brown food-webs: Animal trophic identity reflects rampant microbivory

(2017) Shawn A. Steffan et al.   Ecology and Evolution

The Role of Microbes in the Nutrition of Detritivorous Invertebrates: A Stoichiometric Analysis

(2017) Thomas R. Anderson et al.   Frontiers in Microbiology

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

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi-arid soils

(2016) Felipe Bastida et al.   MOLECULAR ECOLOGY

The interdependence of transcript and protein abundance: new data-new complexities

(2016) Y. Liu et al.   Molecular Systems Biology

Bacteria dominate the short-term assimilation of plant-derived N in soil

(2016) Robert Starke et al.   SOIL BIOLOGY & BIOCHEMISTRY

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

(2016) Ernesto S. Nakayasu et al.   mSystems

Quantitative Microbial Ecology through Stable Isotope Probing

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

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition

(2015) Salvador Lladó et al.   BIOLOGY AND FERTILITY OF SOILS

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

(2015) Lucia Žifčáková et al.   ENVIRONMENTAL MICROBIOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Dietary and taxonomic controls on incorporation of microbial carbon and phosphorus by detritivorous caddisflies

(2015) Halvor M. Halvorson et al.   OECOLOGIA

A decade of metaproteomics: Where we stand and what the future holds

(2015) Paul Wilmes et al.   PROTEOMICS

Navigating through metaproteomics data: A logbook of database searching

(2015) Thilo Muth et al.   PROTEOMICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Metaproteomics of soils from semiarid environment: Functional and phylogenetic information obtained with different protein extraction methods

(2014) F. Bastida et al.   Journal of Proteomics

Forests trapped in nitrogen limitation - an ecological market perspective on ectomycorrhizal symbiosis

(2014) Oskar Franklin et al.   NEW PHYTOLOGIST

Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling

(2014) Maria Mooshammer et al.   Nature Communications

Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities

(2013) Robert L. Hettich et al.   ANALYTICAL CHEMISTRY

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

(2013) Anthony Levasseur et al.   Biotechnology for Biofuels

Nitrate and periplasmic nitrate reductases

(2013) Courtney Sparacino-Watkins et al.   CHEMICAL SOCIETY REVIEWS

Tracing the biosynthetic source of essential amino acids in marine turtles using δ13C fingerprints

(2013) Karen E. Arthur et al.   ECOLOGY

Carbon and nitrogen pools and fluxes above and below ground in spruce, pine and birch stands in southern Sweden

(2013) Karna Hansson et al.   FOREST ECOLOGY AND MANAGEMENT

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology

(2013) Martin von Bergen et al.   ISME Journal

Aging, hypertension and physiological tremor: The contribution of the cardioballistic impulse to tremorgenesis in older adults

(2013) Steven Morrison et al.   JOURNAL OF THE NEUROLOGICAL SCIENCES

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

Processes regulating nitric oxide emissions from soils

(2013) K. Pilegaard   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Biological nitrogen fixation: rates, patterns and ecological controls in terrestrial ecosystems

(2013) P. M. Vitousek et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Towards a climate-dependent paradigm of ammonia emission and deposition

(2013) M. A. Sutton et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Discovery of Glycoside Hydrolase Enzymes in an Avicel-Adapted Forest Soil Fungal Community by a Metatranscriptomic Approach

(2013) Kazuto Takasaki et al.   PLoS One

Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest

(2013) K. E. Clemmensen et al.   SCIENCE

Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations

(2012) Jörg Simon et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

(2012) Martina Štursová et al.   FEMS MICROBIOLOGY ECOLOGY

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions

(2012) Thomas Schneider et al.   ISME Journal

Soil proteomics: An assessment of its potential for archaeological site interpretation

(2012) S. Oonk et al.   ORGANIC GEOCHEMISTRY

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

(2012) Coralie Damon et al.   PLoS One

Soil metaproteomics – Comparative evaluation of protein extraction protocols

(2012) Katharina M. Keiblinger et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil enzymes in a changing environment: Current knowledge and future directions

(2012) Richard G. Burns et al.   SOIL BIOLOGY & BIOCHEMISTRY

Cultivation of unculturable soil bacteria

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

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

(2011) Petr Baldrian et al.   ISME Journal

Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil

(2011) J. Pratscher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Y. Pan et al.   SCIENCE

Guidelines for experimental design and data analysis of proteomic mass spectrometry-based experiments

(2010) Karin Barnouin   AMINO ACIDS

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

(2010) Frank Rasche et al.   ISME Journal

Various players in the nitrogen cycle: Diversity and functions of the microorganisms involved in nitrification and denitrification

(2010) Masahito Hayatsu et al.   SOIL SCIENCE AND PLANT NUTRITION

Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil

(2009) L. M. Feinstein et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Stable isotope fingerprinting: a novel method for identifying plant, fungal, or bacterial origins of amino acids

(2009) Thomas Larsen et al.   ECOLOGY

Fine root decomposition rates do not mirror those of leaf litter among temperate tree species

(2009) Sarah E. Hobbie et al.   OECOLOGIA

Trophic structure and major trophic links in conventional versus organic farming systems as indicated by carbon stable isotope ratios of fatty acids

(2009) Dominique Haubert et al.   OIKOS

Compartmentalization of the soil animal food web as indicated by dual analysis of stable isotope ratios (15N/14N and 13C/12C)

(2009) Melanie M. Pollierer et al.   SOIL BIOLOGY & BIOCHEMISTRY

Structure and Action Mechanism of Ligninolytic Enzymes

(2008) Dominic W. S. Wong   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

(2008) A. M. Mayampurath et al.   BIOINFORMATICS

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH