Microbial community composition in the rhizosphere of Larix decidua under different light regimes with additional focus on methane cycling microorganisms

Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China

(2020) Yuanfeng Cai et al.   MICROBIAL ECOLOGY

Divergent drivers of the microbial methane sink in temperate forest and grassland soils

(2020) Jana Täumer et al.   GLOBAL CHANGE BIOLOGY

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

(2019) Bojk A. Berghuis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of temperature on the microbial community responsible for methane production in alkaline NamCo wetland soil

(2019) Yongcui Deng et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient

(2019) Nadine Praeg et al.   Frontiers in Microbiology

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane-Oxidizing Upland Soil Cluster α

(2018) Jennifer Pratscher et al.   ENVIRONMENTAL MICROBIOLOGY

The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence

(2018) Francesca Mapelli et al.   ISME Journal

Living apart together—bacterial volatiles influence methanotrophic growth and activity

(2018) A. J. Veraart et al.   ISME Journal

Water stress limits transpiration and growth of European larch up to the lower subalpine belt in an inner-alpine dry valley

(2018) Nikolaus Obojes et al.   NEW PHYTOLOGIST

Effects of Drought and Salinity on European Larch (Larix decidua Mill.) Seedlings

(2018) Ioana Plesa et al.   Forests

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon

(2018) Evan P. Starr et al.   Microbiome

Characteristics of bulk and rhizosphere soil microbial community in an ancient Platycladus orientalis forest

(2018) Jinliang Liu et al.   APPLIED SOIL ECOLOGY

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

(2017) Panagiotis S Adam et al.   ISME Journal

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

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

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Plant species, temperature, and bedrock affect net methane flux out of grassland and forest soils

(2016) Nadine Praeg et al.   PLANT AND SOIL

Bacterial populations in juvenile maize rhizospheres originate from both seed and soil

(2016) David Johnston-Monje et al.   PLANT AND SOIL

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils

(2016) Yuanfeng Cai et al.   Nature Communications

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

(2016) Adrian Ho et al.   Frontiers in Microbiology

The Ecology of Acidobacteria: Moving beyond Genes and Genomes

(2016) Anna M. Kielak et al.   Frontiers in Microbiology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

(2016) Tess E. Brewer et al.   Nature Microbiology

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities

(2016) S. Uroz et al.   Scientific Reports

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia

(2016) Bruno L. Mello et al.   Scientific Reports

Methylocapsa palsarum sp. nov., a methanotroph isolated from a subArctic discontinuous permafrost ecosystem

(2015) Svetlana N. Dedysh et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

(2015) Andrzej Tkacz et al.   ISME Journal

Water availability and abundance of microbial groups are key determinants of greenhouse gas fluxes in a dryland forest ecosystem

(2015) Catarina S.C. Martins et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial hotspots and hot moments in soil: Concept & review

(2015) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

(2015) Claudia Knief   Frontiers in Microbiology

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Insights into the distribution and abundance of the ubiquitous Candidatus Saccharibacteria phylum following tag pyrosequencing

(2014) Belinda Ferrari et al.   Scientific Reports

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

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

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

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

(2013) Johan Bengtsson-Palme et al.   Methods in Ecology and Evolution

Environmental impacts on the diversity of methane-cycling microbes and their resultant function

(2013) Emma L. Aronson et al.   Frontiers in Microbiology

A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system

(2012) Cindy D. C. Barillot et al.   ANNALS OF MICROBIOLOGY

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Archaeal abundance in relation to root and fungal exudation rates

(2012) Anna E. Karlsson et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

Stimulation of Methanotrophic Growth in Cocultures by Cobalamin Excreted by Rhizobia

(2011) Hiroyuki Iguchi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USCα clade

(2011) Jennifer Pratscher et al.   ENVIRONMENTAL MICROBIOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils

(2011) Heiko Nacke et al.   PLoS One

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil

(2010) Stéphane Uroz et al.   Environmental Microbiology Reports

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

Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere

(2009) Gabriele Berg et al.   FEMS MICROBIOLOGY ECOLOGY

ABC transporters: the power to change

(2009) Douglas C. Rees et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Environmental, genomic and taxonomic perspectives on methanotrophicVerrucomicrobia

(2009) Huub J. M. Op den Camp et al.   Environmental Microbiology Reports

The quest for atmospheric methane oxidizers in forest soils

(2009) Steffen Kolb   Environmental Microbiology Reports

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

Plant host habitat and root exudates shape soil bacterial community structure

(2008) Feth el Zahar Haichar et al.   ISME Journal

Culture-Independent Assessment of Rhizobiales-Related Alphaproteobacteria and the Diversity of Methylobacterium in the Rhizosphere and Rhizoplane of Transgenic Eucalyptus

(2008) Fernando Dini Andreote et al.   MICROBIAL ECOLOGY