Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti

(2020) Víctor M. Flores-Núñez et al.   Frontiers in Microbiology

A plant genetic network for preventing dysbiosis in the phyllosphere

(2020) Tao Chen et al.   NATURE

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest

(2020) Geneviève Lajoie et al.   Microbiome

Microbial functional traits in phyllosphere are more sensitive to anthropogenic disturbance than in soil

(2020) Qian Xiang et al.   ENVIRONMENTAL POLLUTION

Streptomyces sp. strain TOR3209: a rhizosphere bacterium promoting growth of tomato by affecting the rhizosphere microbial community

(2020) Dong Hu et al.   Scientific Reports

Draft Genome Analysis Offers Insights Into the Mechanism by Which Streptomyces chartreusis WZS021 Increases Drought Tolerance in Sugarcane

(2019) Zhen Wang et al.   Frontiers in Microbiology

Driving factors of epiphytic bacterial communities: A review

(2019) Rudolf O. Schlechter et al.   Journal of Advanced Research

SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline

(2019) Javier Tamames et al.   Frontiers in Microbiology

Leaf-associated microbiomes of grafted tomato plants

(2019) Hirokazu Toju et al.   Scientific Reports

Growth and differentiation properties of pikromycin-producing Streptomyces venezuelae ATCC15439

(2019) Ji-Eun Kim et al.   JOURNAL OF MICROBIOLOGY

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

(2019) Samiran Banerjee et al.   ISME Journal

Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition

(2019) Huahua Li et al.   Biotechnology for Biofuels

The tea leaf microbiome shows specific responses to chemical pesticides and biocontrol applications

(2019) Tomislav Cernava et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Soil Photosynthetic Microbial Communities Mediate Aggregate Stability: Influence of Cropping Systems and Herbicide Use in an Agricultural Soil

(2019) Olivier Crouzet et al.   Frontiers in Microbiology

The Nitrate Assimilatory Pathway in Sinorhizobium meliloti: Contribution to NO Production

(2019) Bryan Ruiz et al.   Frontiers in Microbiology

Consortium of Plant Growth-Promoting Rhizobacteria Strains Suppresses Sweet Pepper Disease by Altering the Rhizosphere Microbiota

(2019) Li-Na Zhang et al.   Frontiers in Microbiology

Metagenomic Functional Shifts to Plant Induced Environmental Changes

(2019) Svetlana N. Yurgel et al.   Frontiers in Microbiology

Natural Farming Improves Soil Quality and Alters Microbial Diversity in a Cabbage Field in Japan

(2019) Jianli Liao et al.   Sustainability

Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species

(2019) Julien Massoni et al.   ISME Journal

Fusarium-Produced Mycotoxins in Plant-Pathogen Interactions

(2019) Lakshmipriya Perincherry et al.   Toxins

Regulation of Antibiotic Production by Signaling Molecules in Streptomyces

(2019) Dekun Kong et al.   Frontiers in Microbiology

Field study reveals core plant microbiota and relative importance of their drivers

(2018) Kelly Hamonts et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum

(2018) Meng Dong et al.   Frontiers in Microbiology

Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity

(2018) Shaun P. Stice et al.   Frontiers in Microbiology

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

(2018) Kyle Hartman et al.   Microbiome

FastSpar: rapid and scalable correlation estimation for compositional data

(2018) Stephen C Watts et al.   BIOINFORMATICS

Biological roles of indole-3-acetic acid in Acinetobacter baumannii

(2018) Huei-Ru Lin et al.   MICROBIOLOGICAL RESEARCH

Branching Out: Alterations in Bacterial Physiology and Virulence Due to Branched-Chain Amino Acid Deprivation

(2018) Julienne C. Kaiser et al.   mBio

Mycolicibacterium smegmatis, Basonym Mycobacterium smegmatis, Expresses Morphological Phenotypes Much More Similar to Escherichia coli Than Mycobacterium tuberculosis in Quantitative Structome Analysis and CryoTEM Examination

(2018) Hiroyuki Yamada et al.   Frontiers in Microbiology

Biological control of bacterial plant diseases with Lactobacillus plantarum strains selected for their broad-spectrum activity

(2018) Núria Daranas et al.   ANNALS OF APPLIED BIOLOGY

Day and night: Metabolic profiles and evolutionary relationships of six axenic non-marine cyanobacteria

(2018) Sabine Eva Will et al.   Genome Biology and Evolution

Effect of Rhizobacterium Rhodopseudomonas palustris Inoculation on Stevia rebaudiana Plant Growth and Soil Microbial Community

(2018) Jiangbing XU et al.   PEDOSPHERE

The effect of moisture on soil microbial properties and nitrogen cyclers in Mediterranean sweet orange orchards under organic and inorganic fertilization

(2018) Alicia Morugán-Coronado et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Influence of resistance breeding in common bean on rhizosphere microbiome composition and function

(2017) Lucas William Mendes et al.   ISME Journal

Organic farming increases richness of fungal taxa in the wheat phyllosphere

(2017) Ida Karlsson et al.   MOLECULAR ECOLOGY

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships

(2017) Isabelle Laforest-Lapointe et al.   NATURE

The influence of fertiliser and pesticide emissions model on life cycle assessment of agricultural products: The case of Danish and Italian barley

(2017) Ximena C. Schmidt Rivera et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Let the Core Microbiota Be Functional

(2017) Philippe Lemanceau et al.   TRENDS IN PLANT SCIENCE

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

(2017) Yun Kit Yeoh et al.   Nature Communications

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

(2017) Manoeli Lupatini et al.   Frontiers in Microbiology

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree

(2016) Omri M. Finkel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Concerns over use of glyphosate-based herbicides and risks associated with exposures: a consensus statement

(2016) John Peterson Myers et al.   Environmental Health

Phyllosphere Metaproteomes of Trees from the Brazilian Atlantic Forest Show High Levels of Functional Redundancy

(2016) M. R. Lambais et al.   MICROBIAL ECOLOGY

Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization

(2016) Daniel B. Müller et al.   MOLECULAR & CELLULAR PROTEOMICS

The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen

(2016) Unyarat Ritpitakphong et al.   NEW PHYTOLOGIST

Carotenoid Biosynthesis inCalothrixsp. 336/3: Composition of Carotenoids on Full Medium, During Diazotrophic Growth and After Long-Term H2Photoproduction

(2016) Sergey Kosourov et al.   PLANT AND CELL PHYSIOLOGY

Chemotaxis signaling systems in model beneficial plant–bacteria associations

(2016) Birgit E. Scharf et al.   PLANT MOLECULAR BIOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas aeruginosa RRALC3 Enhances the Biomass, Nutrient and Carbon Contents of Pongamia pinnata Seedlings in Degraded Forest Soil

(2015) Parthasarathy Radhapriya et al.   PLoS One

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere

(2015) Chanyarat Paungfoo-Lonhienne et al.   Scientific Reports

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Optimization ofAspergillus nigerrock phosphate solubilization in solid-state fermentation and use of the resulting product as a P fertilizer

(2015) Gilberto de Oliveira Mendes et al.   Microbial Biotechnology

Resilience of the Natural Phyllosphere Microbiota of the Grapevine to Chemical and Biological Pesticides

(2014) Michele Perazzolli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Spatial distribution analyses of natural phyllosphere-colonizing bacteria onArabidopsis thalianarevealed by fluorescencein situhybridization

(2014) Mitja N. P. Remus-Emsermann et al.   ENVIRONMENTAL MICROBIOLOGY

Distinct soil microbial diversity under long-term organic and conventional farming

(2014) Martin Hartmann et al.   ISME Journal

Flavobacterium branchiophilumandF. succinicansassociated with bacterial gill disease in rainbow troutOncorhynchus mykiss(Walbaum) in water recirculation aquaculture systems

(2014) C Good et al.   JOURNAL OF FISH DISEASES

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Fungicide Effects on Fungal Community Composition in the Wheat Phyllosphere

(2014) Ida Karlsson et al.   PLoS One

Biodiversity conservation in agriculture requires a multi-scale approach

(2014) D. J. Gonthier et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The foliar microbiome

(2014) Josep Peñuelas et al.   TRENDS IN PLANT SCIENCE

Ecological Succession and Stochastic Variation in the Assembly of Arabidopsis thaliana Phyllosphere Communities

(2014) L. Maignien et al.   mBio

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Isolation of Optically Targeted Single Bacteria by Application of Fluidic Force Microscopy to Aerobic Anoxygenic Phototrophs from the Phyllosphere

(2013) P. Stiefel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Progress in cultivation-independent phyllosphere microbiology

(2013) Thomas Müller et al.   FEMS MICROBIOLOGY ECOLOGY

Genomic and Enzymatic Results Show Bacillus cellulosilyticus Uses a Novel Set of LPXTA Carbohydrases to Hydrolyze Polysaccharides

(2013) David Mead et al.   PLoS One

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

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

The influence of inorganic nitrogen fertilizer forms on micronutrient retranslocation and accumulation in grains of winter wheat

(2013) Nunun Barunawati et al.   Frontiers in Plant Science

A new species ofBurkholderiaisolated from sugarcane roots promotes plant growth

(2013) Chanyarat Paungfoo-Lonhienne et al.   Microbial Biotechnology

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

(2012) John H Morris et al.   BMC BIOINFORMATICS

Genome Sequences of Burkholderia sp. Strains CCGE1002 and H160, Isolated from Legume Nodules in Mexico and Brazil

(2012) E. Ormeno-Orrillo et al.   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

A Coevolutionary Framework for Managing Disease-Suppressive Soils

(2011) Linda L. Kinkel et al.   Annual Review of Phytopathology

A novel cold-active xylanase from the cellulolytic myxobacterium Sorangium cellulosum So9733-1: gene cloning, expression, and enzymatic characterization

(2011) Shu-Yun Wang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

(2011) Claudia Knief et al.   ISME Journal

Complete Genome Sequences of Krokinobactersp. Strain 4H-3-7-5 and Lacinutrixsp. Strain 5H-3-7-4, Polysaccharide-Degrading Members of the Family Flavobacteriaceae

(2011) B. Klippel et al.   JOURNAL OF BACTERIOLOGY

Structural Basis of Cyanobacterial Photosystem II Inhibition by the Herbicide Terbutryn

(2011) Matthias Broser et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The potential of epiphytic hydrocarbon-utilizing bacteria on legume leaves for attenuation of atmospheric hydrocarbon pollutants

(2011) Nida Ali et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Strategies for engineering a two-celled C4 photosynthetic pathway into rice

(2011) K. Kajala et al.   JOURNAL OF EXPERIMENTAL BOTANY

Nitrate Paradigm Does Not Hold Up for Sugarcane

(2011) Nicole Robinson et al.   PLoS One

New and revisited species in Aspergillus section Nigri

(2011) J. Varga et al.   STUDIES IN MYCOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Screening of plant growth promoting traits ofBacillus thuringiensis

(2010) Noura Raddadi et al.   ANNALS OF MICROBIOLOGY

The solubilization of potassium-bearing rock powder by Aspergillus niger in small-scale batch fermentations

(2010) Maria L. Lopes-Assad et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Metallosphaera cuprina sp. nov., an acidothermophilic, metal-mobilizing archaeon

(2010) L.-J. Liu et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content

(2010) Alessandro J. Waclawovsky et al.   PLANT BIOTECHNOLOGY JOURNAL

Enteric Fever-Like Syndrome Caused by Raoultella ornithinolytica (Klebsiella ornithinolytica)

(2009) V. Pulian Morais et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees

(2008) S. Taghavi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Nitrogen fixation by phyllosphere bacteria associated with higher plants and their colonizing epiphytes of a tropical lowland rainforest of Costa Rica

(2008) Michael Fürnkranz et al.   ISME Journal

Agricultural sustainability: concepts, principles and evidence

(2007) J. Pretty   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES