Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

(2018) Julia Hassa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on β-1,2-Glucooligosaccharides from Parabacteroides distasonis

(2018) Hisaka Shimizu et al.   BIOCHEMISTRY

Metagenomic analysis of microbial community and function involved in cd-contaminated soil

(2018) Gang Feng et al.   BMC MICROBIOLOGY

Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia

(2018) Ruben Garrido-Oter et al.   Cell Host & Microbe

Connecting microbial capabilities with the soil and plant health: Options for agricultural sustainability

(2018) Pramod K. Sahu et al.   ECOLOGICAL INDICATORS

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

(2018) Stephanie A. Eichorst et al.   ENVIRONMENTAL MICROBIOLOGY

Arbuscular mycorrhizal fungi as mediators of ecosystem responses to nitrogen deposition: A trait-based predictive framework

(2018) Kathleen K. Treseder et al.   JOURNAL OF ECOLOGY

Microbial volatiles as plant growth inducers

(2018) Paola Fincheira et al.   MICROBIOLOGICAL RESEARCH

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing

(2018) Loreen Sommermann et al.   PLoS One

Current Trends in Methylotrophy

(2018) Ludmila Chistoserdova et al.   TRENDS IN MICROBIOLOGY

Flexible metagenome analysis using the MGX framework

(2018) Sebastian Jaenicke et al.   Microbiome

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

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

Plant growth promoting bacteria: role in soil improvement, abiotic and biotic stress management of crops

(2018) Abdul Majeed et al.   PLANT CELL REPORTS

A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera

(2018) Radhey S. Gupta et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Rhizosphere microbiome structure alters to enable wilt resistance in tomato

(2018) Min-Jung Kwak et al.   NATURE BIOTECHNOLOGY

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

LUCAS Soil, the largest expandable soil dataset for Europe: a review

(2017) A. Orgiazzi et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Biochemical and structural analyses of a bacterialendo-β-1,2-glucanase reveal a new glycoside hydrolase family

(2017) Koichi Abe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bioinformatics for NGS-based metagenomics and the application to biogas research

(2017) Sebastian Jünemann et al.   JOURNAL OF BIOTECHNOLOGY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils

(2017) Ruth Gómez Expósito et al.   Frontiers in Microbiology

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity

(2017) Emma Ransom-Jones et al.   mSphere

Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria

(2016) Anna M. Kielak et al.   ARCHIVES OF MICROBIOLOGY

The quorum sensing moleculeN-acyl homoserine lactone produced byAcinetobacter baumanniidisplays antibacterial and anticancer properties

(2016) James John et al.   BIOFOULING

Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions

(2016) Martha Zakrzewski et al.   BIOINFORMATICS

Aryl Polyenes, a Highly Abundant Class of Bacterial Natural Products, Are Functionally Related to Antioxidative Carotenoids

(2016) Tim A. Schöner et al.   CHEMBIOCHEM

New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase

(2016) Bram Vekeman et al.   ENVIRONMENTAL MICROBIOLOGY

Isolation of acetic, propionic and butyric acid-forming bacteria from biogas plants

(2016) Katharina Gabriela Cibis et al.   JOURNAL OF BIOTECHNOLOGY

Bacteriocins and the assembly of natural Pseudomonas fluorescens populations

(2016) J. B. Bruce et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

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

RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots

(2016) V. C. S. Pankievicz et al.   PLANT MOLECULAR BIOLOGY

Methylotrophic bacteria in sustainable agriculture

(2016) Manish Kumar et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Siderophores: More than Stealing Iron

(2016) Judith Behnsen et al.   mBio

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere

(2016) Marco Kai et al.   Frontiers in Microbiology

The Ecology of Acidobacteria: Moving beyond Genes and Genomes

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

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

(2016) Hsin-Hung Lin et al.   Scientific Reports

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

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

A review of the effects of soil organisms on plant hormone signalling pathways

(2015) Ruben Puga-Freitas et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Community composition and population genetics of insect pathogenic fungi in the genusMetarhiziumfrom soils of a long-term agricultural research system

(2015) Ryan M. Kepler et al.   ENVIRONMENTAL MICROBIOLOGY

Plant growth-promoting bacteria as inoculants in agricultural soils

(2015) Rocheli de Souza et al.   GENETICS AND MOLECULAR BIOLOGY

Volatile affairs in microbial interactions

(2015) Ruth Schmidt et al.   ISME Journal

The GH130 Family of Mannoside Phosphorylases Contains Glycoside Hydrolases That Target β-1,2-Mannosidic Linkages inCandidaMannan

(2015) Fiona Cuskin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association

(2015) Gloria Torres-Cortés et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees

(2015) Henry Müller 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

Environmental Variables Shaping the Ecological Niche of Thaumarchaeota in Soil: Direct and Indirect Causal Effects

(2015) Jin-Kyung Hong et al.   PLoS One

Biodegradable plastic agricultural mulches and key features of microbial degradation

(2014) Marion Brodhagen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla

(2014) Harald Cederlund et al.   APPLIED SOIL ECOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

Recent advances in genome-based polyketide discovery

(2014) Eric JN Helfrich et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bacterial endophyte Sphingomonas sp. LK11 produces gibberellins and IAA and promotes tomato plant growth

(2014) Abdul Latif Khan et al.   JOURNAL OF MICROBIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

(2014) M. Konneke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce

(2014) Susanne Schreiter et al.   Frontiers in Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Structure and Functions of the Bacterial Microbiota of Plants

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

Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

(2013) Mariana Silvia Cretoiu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biochar of animal origin: a sustainable solution to the global problem of high-grade rock phosphate scarcity?

(2013) Nikolay Vassilev et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Bacteria with ACC deaminase can promote plant growth and help to feed the world

(2013) Bernard R. Glick   MICROBIOLOGICAL RESEARCH

Nitric oxide as a key component in hormone-regulated processes

(2013) Marcela Simontacchi et al.   PLANT CELL REPORTS

Metagenomics and novel gene discovery

(2013) Eamonn P Culligan et al.   Virulence

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

(2013) Kateryna Zhalnina et al.   Frontiers in Microbiology

Gibberellin biosynthesis and its regulation

(2012) Peter Hedden et al.   BIOCHEMICAL JOURNAL

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Global food security, biodiversity conservation and the future of agricultural intensification

(2012) Teja Tscharntke et al.   BIOLOGICAL CONSERVATION

Plant growth-promoting rhizobacteria (PGPR): their potential as antagonists and biocontrol agents

(2012) Anelise Beneduzi et al.   GENETICS AND MOLECULAR BIOLOGY

Type III polyketide synthases in natural product biosynthesis

(2012) Dayu Yu et al.   IUBMB LIFE

Malleilactone, a Polyketide Synthase-Derived Virulence Factor Encoded by the Cryptic Secondary Metabolome of Burkholderia pseudomallei Group Pathogens

(2012) John B. Biggins et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Soil Suppressiveness to Fusarium Disease: Shifts in Root Microbiome Associated with Reduction of Pathogen Root Colonization

(2012) Eyal Klein et al.   PHYTOPATHOLOGY

The Multifactorial Basis for Plant Health Promotion by Plant-Associated Bacteria

(2011) Young Cheol Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Organic inputs, tillage and rotation practices influence soil health and suppressiveness to soilborne pests and pathogens of ginger

(2011) G. R. Stirling et al.   AUSTRALASIAN PLANT PATHOLOGY

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

(2011) Michael Pester et al.   CURRENT OPINION IN MICROBIOLOGY

The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica

(2011) Lars Ganzert et al.   FEMS MICROBIOLOGY ECOLOGY

Toward an Efficient Method of Identifying Core Genes for Evolutionary and Functional Microbial Phylogenies

(2011) Nicola Segata et al.   PLoS One

Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil

(2011) M. Tourna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Long-term effects of tillage on stratification and plant availability of phosphate and potassium in a loess chernozem

(2011) Annette Deubel et al.   SOIL & TILLAGE RESEARCH

Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules

(2010) Jacob J Banik et al.   CURRENT OPINION IN MICROBIOLOGY

Biodiversity is associated with indicators of soil ecosystem functions over a landscape gradient of agricultural intensification

(2010) Steven W. Culman et al.   LANDSCAPE ECOLOGY

Community profiling and quantification of putative autotrophic thaumarchaeal communities in environmental samples

(2010) Pierre Offre et al.   Environmental Microbiology Reports

Plant–microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture

(2009) Gabriele Berg   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Soil microbial activity and crop sustainability in a long-term experiment with three soil-tillage and two crop-rotation systems

(2009) Mariangela Hungria et al.   APPLIED SOIL ECOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Phylogenetic diversity of Acidobacteria in a former agricultural soil

(2008) Anna Kielak et al.   ISME Journal