Bog ecosystems as a playground for plant–microbe coevolution: bryophytes and vascular plants harbour functionally adapted bacteria

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

(2021) Francesco Durazzi et al.   Scientific Reports

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

(2020) Jasmine Chong et al.   Nature Protocols

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

(2020) Xinyu Zhu et al.   Microbiome

Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves

(2020) Julian Regalado et al.   ISME Journal

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

(2020) Francesco Asnicar et al.   Nature Communications

Massive peatland carbon banks vulnerable to rising temperatures

(2020) A. M. Hopple et al.   Nature Communications

Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils

(2020) Houpu Zhang et al.   JOURNAL OF HAZARDOUS MATERIALS

What is new and relevant for sequencing-based microbiome research? A minireview

(2019) Alena M. Fricker et al.   Journal of Advanced Research

A plant perspective on nitrogen cycling in the rhizosphere

(2019) Delphine Moreau et al.   FUNCTIONAL ECOLOGY

Ecology and Evolution of Plant Microbiomes

(2019) Viviane Cordovez et al.   Annual Review of Microbiology

Defining the Genetic Basis of Plant–Endophytic Bacteria Interactions

(2019) Artur Pinski et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.)

(2019) Julian Taffner et al.   Journal of Advanced Research

Experimental warming alters the community composition, diversity, and N 2 fixation activity of peat moss ( Sphagnum fallax ) microbiomes

(2019) Alyssa A. Carrell et al.   GLOBAL CHANGE BIOLOGY

The molecular chaperone Hsp33 is activated by atmospheric-pressure plasma protecting proteins from aggregation

(2019) Marco Krewing et al.   Journal of the Royal Society Interface

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

KEGG Mapper for inferring cellular functions from protein sequences

(2019) Minoru Kanehisa et al.   PROTEIN SCIENCE

Ammonia stress reduces antibiotic efflux but enriches horizontal gene transfer of antibiotic resistance genes in anaerobic digestion

(2019) Junya Zhang et al.   BIORESOURCE TECHNOLOGY

Biotic and Abiotic Drivers of Peatland Growth and Microtopography: A Model Demonstration

(2018) Nitin Chaudhary et al.   ECOSYSTEMS

Novel bacterial lineages associated with boreal moss species

(2018) Hannah Holland-Moritz et al.   ENVIRONMENTAL MICROBIOLOGY

Methanotrophy across a natural permafrost thaw environment

(2018) Caitlin M Singleton et al.   ISME Journal

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

(2018) Julian Taffner et al.   mSphere

NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

(2018) Qichao Tu et al.   BIOINFORMATICS

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

Marchantia liverworts as a proxy to plants’ basal microbiomes

(2018) Luis D. Alcaraz et al.   Scientific Reports

Host-pathogen biotic interactions shaped vitamin K metabolism in Archaeplastida

(2018) U. Cenci et al.   Scientific Reports

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

(2017) Achal Dhariwal et al.   NUCLEIC ACIDS RESEARCH

Taxonomic and functional turnover are decoupled in European peat bogs

(2017) Bjorn J. M. Robroek et al.   Nature Communications

Double-Face Meets the Bacterial World: The Opportunistic Pathogen Stenotrophomonas maltophilia

(2017) Felipe Lira et al.   Frontiers in Microbiology

The Pathogenic Potential of a Microbe

(2017) Arturo Casadevall   mSphere

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics

(2016) Viktor Jonsson et al.   BMC GENOMICS

Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms

(2016) Bela Hausmann et al.   ISME Journal

Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems

(2016) Tin Mar Lynn et al.   MICROBIAL ECOLOGY

The Sphagnum microbiome: new insights from an ancient plant lineage

(2016) Joel E. Kostka et al.   NEW PHYTOLOGIST

Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity

(2015) Barbara Reinhold-Hurek et al.   Annual Review of Phytopathology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

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

(2015) Dinghua Li et al.   BIOINFORMATICS

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

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

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

The plant microbiome explored: implications for experimental botany

(2015) Gabriele Berg et al.   JOURNAL OF EXPERIMENTAL BOTANY

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity

(2015) Anastasia Bragina et al.   MOLECULAR ECOLOGY

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa

(2015) S. L. Lebeis et al.   SCIENCE

TheSphagnummicrobiome supports bog ecosystem functioning under extreme conditions

(2014) Anastasia Bragina et al.   MOLECULAR ECOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Sphagnum Mosses - Masters of Efficient N-Uptake while Avoiding Intoxication

(2014) Christian Fritz et al.   PLoS One

Fine-scale dynamics and community stability in boreal peatlands: revisiting a fen and a bog in Sweden after 50 years

(2014) E. Pedrotti et al.   Ecosphere

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Activation of Defense Mechanisms against Pathogens in Mosses and Flowering Plants

(2013) Inés Ponce de León et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

(2013) Thomas R Turner et al.   ISME Journal

Endophytic bacteria of Sphagnum mosses as promising objects of agricultural microbiology

(2013) A. V. Shcherbakov et al.   MICROBIOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Ammonium first: natural mosses prefer atmospheric ammonium but vary utilization of dissolved organic nitrogen depending on habitat and nitrogen deposition

(2013) Xue-Yan Liu et al.   NEW PHYTOLOGIST

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

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

Methanotrophy induces nitrogen fixation during peatland development

(2013) T. Larmola et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into functional bacterial diversity and its effects on Alpine bog ecosystem functioning

(2013) Anastasia Bragina et al.   Scientific Reports

Significant Role for Microbial Autotrophy in the Sequestration of Soil Carbon

(2012) Hongzhao Yuan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Similar Diversity of Alphaproteobacteria and Nitrogenase Gene Amplicons on Two Related Sphagnum Mosses

(2012) Anastasia Bragina et al.   Frontiers in Microbiology

Initiation of Sphagnum moss hummocks in bogs and the presence of vascular plants: Is there a link?

(2011) Rémy Pouliot et al.   ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY

Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat

(2011) Timofey A. Pankratov et al.   ENVIRONMENTAL MICROBIOLOGY

Sphagnum mosses harbour highly specific bacterial diversity during their whole lifecycle

(2011) Anastasia Bragina et al.   ISME Journal

A holistic view of nitrogen acquisition in plants

(2011) T. Kraiser et al.   JOURNAL OF EXPERIMENTAL BOTANY

RNA-Seq methods for imperfect samples: development, evaluation and applications

(2011) Xian Adiconis et al.   GENOME BIOLOGY

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

(2010) Michael Hügler et al.   Annual Review of Marine Science

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

Peatland Response to Global Change

(2009) N. B. Dise   SCIENCE

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

(2009) Stéphane Compant et al.   SOIL BIOLOGY & BIOCHEMISTRY