Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis

(2016) Firouz Abbasian et al.   BIOTECHNOLOGY PROGRESS

Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal (AMF) community determine assemblages of the AMF spore-associated microbes

(2016) Bachir Iffis et al.   ENVIRONMENTAL MICROBIOLOGY

The glucose metabolite methylglyoxal inhibits expression of the glucose transporter genes by inactivating the cell surface glucose sensors Rgt2 and Snf3 in yeast

(2016) Adhiraj Roy et al.   MOLECULAR BIOLOGY OF THE CELL

Igneous phosphate rock solubilization by biofilm-forming mycorrhizobacteria and hyphobacteria associated with Rhizoglomus irregulare DAOM 197198

(2016) Salma Taktek et al.   MYCORRHIZA

Accounting for reciprocal host–microbiome interactions in experimental science

(2016) Thaddeus S. Stappenbeck et al.   NATURE

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance inSalixsp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants

(2016) Nicholas J. B. Brereton et al.   PLANT PHYSIOLOGY

Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray

(2016) Fabiano Sillo et al.   PLANTA

Basidiomycete yeasts in the cortex of ascomycete macrolichens

(2016) Toby Spribille et al.   SCIENCE

Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza

(2016) Kevin Garcia et al.   TRENDS IN PLANT SCIENCE

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

(2016) Martina Peter et al.   Nature Communications

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds

(2016) Pui Yi Yung et al.   Scientific Reports

Back to the Future of Soil Metagenomics

(2016) Joseph Nesme et al.   Frontiers in Microbiology

Arbuscular mycorrhiza Symbiosis Induces a Major Transcriptional Reprogramming of the Potato SWEET Sugar Transporter Family

(2016) Jasmin Manck-Götzenberger et al.   Frontiers in Plant Science

Revisiting operons: an analysis of the landscape of transcriptional units in E. coli

(2015) Xizeng Mao et al.   BMC BIOINFORMATICS

Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs

(2015) Carlos Villacorta-Martin et al.   BMC GENOMICS

Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil

(2015) Emmanuel Gonzalez et al.   BMC PLANT BIOLOGY

X-ray micro-computed tomography in willow reveals tissue patterning of reaction wood and delay in programmed cell death

(2015) Nicholas Brereton et al.   BMC PLANT BIOLOGY

Enzymatic synthesis and modification of surface-active glycolipids

(2015) Martin Pöhnlein et al.   EUROPEAN JOURNAL OF LIPID SCIENCE AND TECHNOLOGY

Comparison of potential diatom ‘barcode’ genes (the 18S rRNA gene and ITS, COI, rbcL) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta

(2015) Liliang Guo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Yeast Pmp3p has an important role in plasma membrane organization

(2015) J. De Block et al.   JOURNAL OF CELL SCIENCE

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

(2015) Annegret Kohler et al.   NATURE GENETICS

Secretion systems in Gram-negative bacteria: structural and mechanistic insights

(2015) Tiago R. D. Costa et al.   NATURE REVIEWS MICROBIOLOGY

Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors

(2015) Firoz Shah et al.   NEW PHYTOLOGIST

The Arabidopsis vacuolar sugar transporter SWEET2 limits carbon sequestration from roots and restrictsPythiuminfection

(2015) Hsin-Yi Chen et al.   PLANT JOURNAL

Polyadenylation inE. coli: a 20 year odyssey

(2015) Sidney R. Kushner   RNA

Symbiotic association betweenSalix purpureaL. andRhizophagus irregularis: modulation of plant responses under copper stress

(2015) Adriana M. Almeida-Rodríguez et al.   TREE PHYSIOLOGY

Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins

(2015) Clement Pellegrin et al.   Frontiers in Microbiology

Transplanting Soil Microbiomes Leads to Lasting Effects on Willow Growth, but not on the Rhizosphere Microbiome

(2015) Etienne Yergeau et al.   Frontiers in Microbiology

Non-coding RNA: what is functional and what is junk?

(2015) Alexander F. Palazzo et al.   Frontiers in Genetics

Construction and basic characterization of deletion mutants of the genes involved in chitin utilization bySerratia marcescens2170

(2014) Shinya Takanao et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

A Stereospecific Pathway Diverts β-Oxidation Intermediates to the Biosynthesis of Rhamnolipid Biosurfactants

(2014) Ahmad Mohammad Abdel-Mawgoud et al.   CHEMISTRY & BIOLOGY

Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment

(2014) Claire Veneault-Fourrey et al.   FUNGAL GENETICS AND BIOLOGY

Structural Data on the Periplasmic Aldehyde Oxidoreductase PaoABC from Escherichia coli: SAXS and Preliminary X-ray Crystallography Analysis

(2014) Ana Otrelo-Cardoso et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

In vitro Scleroderma laeveandEucalyptus grandismycorrhization and analysis ofatp6, 17S rDNA, andrasgene expression during ectomycorrhizal formation

(2014) Maíra de Freitas Pereira et al.   JOURNAL OF BASIC MICROBIOLOGY

Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes

(2014) Johanna Rytioja et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Membrane Trafficking Pathways and their Roles in Plant–Microbe Interactions

(2014) Noriko Inada et al.   PLANT AND CELL PHYSIOLOGY

Insertions or Deletions (Indels) in the rrn 16S-23S rRNA Gene Internal Transcribed Spacer Region (ITS) Compromise the Typing and Identification of Strains within the Acinetobacter calcoaceticus-baumannii (Acb) Complex and Closely Related Members

(2014) Christopher Maslunka et al.   PLoS One

Contrasting the Community Structure of Arbuscular Mycorrhizal Fungi from Hydrocarbon-Contaminated and Uncontaminated Soils following Willow (Salix spp. L.) Planting

(2014) Saad El-Din Hassan et al.   PLoS One

Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes

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

Increasing phytoremediation efficiency and reliability using novel omics approaches

(2014) Terrence H. Bell et al.   TRENDS IN BIOTECHNOLOGY

Gains of Bacterial Flagellar Motility in a Fungal World

(2013) Martin Pion et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

(2013) Andrea Porras-Alfaro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Structure and Function of Carbohydrate-Binding Module Families 13 and 42 of Glycoside Hydrolases, Comprising a β-Trefoil Fold

(2013) Zui FUJIMOTO   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Nitrate and periplasmic nitrate reductases

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

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

(2013) Etienne Yergeau et al.   ISME Journal

Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny

(2013) Terrence H Bell et al.   ISME Journal

YfdW and YfdU Are Required for Oxalate-Induced Acid Tolerance in Escherichia coli K-12

(2013) E. M. Fontenot et al.   JOURNAL OF BACTERIOLOGY

Functional Profiling and Distribution of the Forest Soil Bacterial Communities Along the Soil Mycorrhizosphere Continuum

(2013) S. Uroz et al.   MICROBIAL ECOLOGY

Plant Expansins in Bacteria and Fungi: Evolution by Horizontal Gene Transfer and Independent Domain Fusion

(2013) Nikolas Nikolaidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fungal host specificity is not a bottleneck for the germination of Pyroleae species (Ericaceae) in a Bavarian forest

(2013) Nicole A. Hynson et al.   MOLECULAR ECOLOGY

Assessment of ectomycorrhizal fungal communities in the natural habitats of Tuber magnatum (Ascomycota, Pezizales)

(2013) M. Leonardi et al.   MYCORRHIZA

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungusPaxillus involutus

(2013) Firoz Shah et al.   NEW PHYTOLOGIST

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

(2013) Jin Duan et al.   PLoS One

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Role of polyadenylation in regulation of the flagella cascade and motility in Escherichia coli

(2012) Alexandre Maes et al.   BIOCHIMIE

Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms

(2012) Alexander Tveit et al.   ISME Journal

Rhamnolipids—Next generation surfactants?

(2012) Markus Michael Müller et al.   JOURNAL OF BIOTECHNOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

Structural insights into the biogenesis and biofilm formation by the Escherichia coli common pilus

(2012) J. A. Garnett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rhamnolipids as biosurfactants from renewable resources: Concepts for next-generation rhamnolipid production

(2012) Marius Henkel et al.   PROCESS BIOCHEMISTRY

Sugar transporters in plants and in their interactions with fungi

(2012) Joan Doidy et al.   TRENDS IN PLANT SCIENCE

Potential of Plants from the Genus Agave as Bioenergy Crops

(2011) Luis Lauro Escamilla-Treviño   BioEnergy Research

Gene regulation of rhamnolipid production in Pseudomonas aeruginosa – A review

(2011) Rodrigo S. Reis et al.   BIORESOURCE TECHNOLOGY

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Role of the Biofilm Master Regulator CsgD in Cross-Regulation between Biofilm Formation and Flagellar Synthesis

(2011) H. Ogasawara et al.   JOURNAL OF BACTERIOLOGY

Enhanced production of trehalose in Escherichia coli by homologous expression of otsBA in the presence of the trehalase inhibitor, validamycin A, at high osmolarity

(2011) He Li et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

(2011) Daniel L. Lindner et al.   MYCOLOGIA

Localization of Cell Wall Polysaccharides in Normal and Compression Wood of Radiata Pine: Relationships with Lignification and Microfibril Orientation

(2011) L. A. Donaldson et al.   PLANT PHYSIOLOGY

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS BIOLOGY

Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica

(2011) Alga Zuccaro et al.   PLoS Pathogens

Distinguishing ectomycorrhizal and saprophytic fungi using carbon and nitrogen isotopic compositions

(2011) Weiguo Hou et al.   Geoscience Frontiers

Impact of Endochitinase-Transformed White Spruce on Soil Fungal Biomass and Ectendomycorrhizal Symbiosis

(2010) F. O. P. Stefani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Techno-economic analysis of lignocellulosic ethanol: A review

(2010) Edgard Gnansounou et al.   BIORESOURCE TECHNOLOGY

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Escherichia coli K-12 possesses multiple cryptic but functional chaperone-usher fimbriae with distinct surface specificities

(2010) Charalampia-Georgia Korea et al.   ENVIRONMENTAL MICROBIOLOGY

AmtB-mediated NH3transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4+/NH3

(2010) Fred C. Boogerd et al.   FEBS LETTERS

Transcribed dark matter: meaning or myth?

(2010) C. P. Ponting et al.   HUMAN MOLECULAR GENETICS

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

(2010) Frank J Stewart et al.   ISME Journal

Mat fimbriae promote biofilm formation by meningitis-associated Escherichia coli

(2010) T. A. Lehti et al.   MICROBIOLOGY-SGM

A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal

(2010) GREGORY M. BONITO et al.   MOLECULAR ECOLOGY

Ectomycorrhizas and water relations of trees: a review

(2010) Tarja Lehto et al.   MYCORRHIZA

Sugar transporters for intercellular exchange and nutrition of pathogens

(2010) Li-Qing Chen et al.   NATURE

Genomic profiling of carbohydrate metabolism in the ectomycorrhizal fungus Tuber melanosporum

(2010) P. Ceccaroli et al.   NEW PHYTOLOGIST

Phytoextraction of heavy metals by two Salicaceae clones in symbiosis with arbuscular mycorrhizal fungi during the second year of a field trial

(2010) Laurence Bissonnette et al.   PLANT AND SOIL

Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

(2010) Safiyh Taghavi et al.   PLoS Genetics

Bacterial/archaeal/organellar polyadenylation

(2010) Bijoy K. Mohanty et al.   Wiley Interdisciplinary Reviews-RNA

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Plants, Mycorrhizal Fungi, and Bacteria: A Network of Interactions

(2009) Paola Bonfante et al.   Annual Review of Microbiology

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

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

A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)

(2009) Rajeev K Varshney et al.   BMC GENOMICS

TheEscherichia coli ycbQRSToperon encodes fimbriae with laminin-binding and epithelial cell adherence properties in Shiga-toxigenicE. coliO157:H7

(2009) Partha Samadder et al.   ENVIRONMENTAL MICROBIOLOGY

Enterobacteriaceae facilitate the anaerobic degradation of glucose by a forest soil

(2009) Daniela M. Degelmann et al.   FEMS MICROBIOLOGY ECOLOGY

The water-deficit stress- and red-rot-related genes in sugarcane

(2009) Vikrant Gupta et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target

(2009) N. Figueroa-Bossi et al.   GENES & DEVELOPMENT

Expansion of signal pathways in the ectomycorrhizal fungus Laccaria bicolor- evolution of nucleotide sequences and expression patterns in families of protein kinases and RAS small GTPases

(2009) Balaji Rajashekar et al.   NEW PHYTOLOGIST

An ABC transport system that maintains lipid asymmetry in the Gram-negative outer membrane

(2009) J. C. Malinverni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The relative value of operon predictions

(2008) R. W. W. Brouwer et al.   BRIEFINGS IN BIOINFORMATICS

Universal and species-specific bacterial ‘fungiphiles’ in the mycospheres of different basidiomycetous fungi

(2008) J. A. Warmink et al.   ENVIRONMENTAL MICROBIOLOGY

Identification of genes responsive to salt stress on Tamarix hispida roots

(2008) Huiyu Li et al.   GENE

High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

(2008) Timo P Sipilä et al.   ISME Journal

RhlA Converts  -Hydroxyacyl-Acyl Carrier Protein Intermediates in Fatty Acid Synthesis to the  -Hydroxydecanoyl- -Hydroxydecanoate Component of Rhamnolipids in Pseudomonas aeruginosa

(2008) K. Zhu et al.   JOURNAL OF BACTERIOLOGY

The importance of chitobiase and N-acetylglucosamine (GlcNAc) uptake in N,N'-diacetylchitobiose [(GlcNAc)2] utilization by Serratia marcescens 2170

(2008) T. Toratani et al.   MICROBIOLOGY-SGM

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

The major pathways of carbohydrate metabolism in the ectomycorrhizal basidiomyceteLaccaria bicolorS238N

(2008) A. Deveau et al.   NEW PHYTOLOGIST

The sugar porter gene family ofLaccaria bicolor: function in ectomycorrhizal symbiosis and soil-growing hyphae

(2008) Mónica Fajardo López et al.   NEW PHYTOLOGIST

A gene repertoire for nitrogen transporters inLaccaria bicolor

(2008) Eva Lucic et al.   NEW PHYTOLOGIST

Ectomycorrhizal fungi and the biotrophy–saprotrophy continuum

(2008) Roger T. Koide et al.   NEW PHYTOLOGIST

Bacterial mycophagy: definition and diagnosis of a unique bacterial–fungal interaction

(2008) Johan H. J. Leveau et al.   NEW PHYTOLOGIST

DOOR: a database for prokaryotic operons

(2008) Fenglou Mao et al.   NUCLEIC ACIDS RESEARCH

A Rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants

(2008) Giorgio Gambino et al.   PHYTOCHEMICAL ANALYSIS

Knock-down of the MEP pathway isogene1-deoxy-d-xylulose 5-phosphate synthase 2inhibits formation of arbuscular mycorrhiza-induced apocarotenoids, and abolishes normal expression of mycorrhiza-specific plant marker genes

(2008) Daniela S. Floß et al.   PLANT JOURNAL