16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages

Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest

(2019) Gileno V. Lacerda-Júnior et al.   Frontiers in Microbiology

Microplot long-term experiment reveals strong soil type influence on bacteria composition and its functional diversity

(2018) Jarosław Grządziel et al.   APPLIED SOIL ECOLOGY

Trichoderma harzianum MTCC 5179 impacts the population and functional dynamics of microbial community in the rhizosphere of black pepper ( Piper nigrum L.)

(2018) Palaniyandi Umadevi et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

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

(2018) Francesca Mapelli et al.   ISME Journal

Mixtures of Plant-Growth-Promoting Rhizobacteria Enhance Biological Control of Multiple Plant Diseases and Plant-Growth Promotion in the Presence of Pathogens

(2018) Ke Liu et al.   PLANT DISEASE

Assembly and ecological function of the root microbiome across angiosperm plant species

(2018) Connor R. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale replicated field study of maize rhizosphere identifies heritable microbes

(2018) William A. Walters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil

(2018) Jing Yuan et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem

(2018) Han Wang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Nitrification and coupled nitrification-denitrification at shallow depths are responsible for early season N 2 O emissions under alternate wetting and drying management in an Italian rice paddy system

(2018) Elizabeth Verhoeven et al.   SOIL BIOLOGY & BIOCHEMISTRY

Phylogenetically distinct methanotrophs modulate methane oxidation in rice paddies across Taiwan

(2018) Yo-Jin Shiau et al.   SOIL BIOLOGY & BIOCHEMISTRY

Nitrite-Oxidizing Bacteria Community Composition and Diversity Are Influenced by Fertilizer Regimes, but Are Independent of the Soil Aggregate in Acidic Subtropical Red Soil

(2018) Shun Han et al.   Frontiers in Microbiology

Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field

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

Influence of Altered Microbes on Soil Organic Carbon Availability in Karst Agricultural Soils Contaminated by Pb-Zn Tailings

(2018) Qiang Li et al.   Frontiers in Microbiology

Drought and host selection influence bacterial community dynamics in the grass root microbiome

(2017) Dan Naylor et al.   ISME Journal

Diversity and composition of rhizospheric soil and root endogenous bacteria inPanax notoginsengduring continuous cropping practices

(2017) Yong Tan et al.   JOURNAL OF BASIC MICROBIOLOGY

The Overproduction of Indole-3-Acetic Acid (IAA) in Endophytes Upregulates Nitrogen Fixation in Both Bacterial Cultures and Inoculated Rice Plants

(2017) Roberto Defez et al.   MICROBIAL ECOLOGY

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice

(2017) Jingna Liu et al.   Scientific Reports

The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard

(2017) Giorgia Novello et al.   Frontiers in Microbiology

Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil

(2017) Annika Vaksmaa et al.   Frontiers in Microbiology

The persistence and performance of phosphate-solubilizing Gluconacetobacter liquefaciens qzr14 in a cucumber soil

(2017) Jingjing Wang et al.   3 Biotech

The persistence and performance of phosphate-solubilizing Gluconacetobacter liquefaciens qzr14 in a cucumber soil

(2017) Jingjing Wang et al.   3 Biotech

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

(2017) Kasie Raymann et al.   mSphere

Comparative analysis of bacterial community structure in the rhizosphere of maize by high-throughput pyrosequencing

(2017) Yi Yang et al.   PLoS One

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage

(2017) Qinghua Qiao et al.   Scientific Reports

Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation

(2017) Shubin He et al.   Scientific Reports

Phosphate-Solubilizing Bacteria Nullify the Antagonistic Effect of Soil Calcification on Bioavailability of Phosphorus in Alkaline Soils

(2017) Muhammad Adnan et al.   Scientific Reports

Safety assessment of antibiotic and probiotic feed additives for Gallus gallus domesticus

(2017) D. P. Neveling et al.   Scientific Reports

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3

(2017) Peng Wang et al.   Scientific Reports

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

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

The succession pattern of soil microbial communities and its relationship with tobacco bacterial wilt

(2016) Jiaojiao Niu et al.   BMC MICROBIOLOGY

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis

(2016) Matthew A. Richards et al.   JOURNAL OF BACTERIOLOGY

Plant root-microbe communication in shaping root microbiomes

(2016) Andrew Lareen et al.   PLANT MOLECULAR BIOLOGY

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach

(2016) P. Bhattacharyya et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes

(2016) Jinping Zhang et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity

(2016) Jichen Wang et al.   Frontiers in Microbiology

The Ecology of Acidobacteria: Moving beyond Genes and Genomes

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

A pmoA-based study reveals dominance of yet uncultured Type I methanotrophs in rhizospheres of an organically fertilized rice field in India

(2016) Pranitha S. Pandit et al.   3 Biotech

A pmoA-based study reveals dominance of yet uncultured Type I methanotrophs in rhizospheres of an organically fertilized rice field in India

(2016) Pranitha S. Pandit et al.   3 Biotech

Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

(2015) Marcela Hernández et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molecular Characterization of Stress Tolerant Plant Growth Promoting Rhizobacteria (PGPR) for Growth Enhancement of Rice

(2015) S.H. Habib et al.   INTERNATIONAL JOURNAL OF AGRICULTURE AND BIOLOGY

Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches

(2015) Pranitha S. Pandit et al.   MICROBIAL ECOLOGY

Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field

(2015) Monali C. Rahalkar et al.   MICROBIAL ECOLOGY

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield

(2015) Thomas Rime et al.   MOLECULAR ECOLOGY

OsIAA6, a member of the rice Aux/IAA gene family, is involved in drought tolerance and tiller outgrowth

(2015) Harin Jung et al.   PLANT SCIENCE

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing

(2015) Wu Xiong et al.   PLoS One

Structure, variation, and assembly of the root-associated microbiomes of rice

(2015) Joseph Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Meta-omics approaches to understand and improve wastewater treatment systems

(2015) Elisa Rodríguez et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

The differential effects of ammonium and nitrate on methanotrophs in rice field soil

(2015) Ang Hu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons

(2015) Shengjing Shi et al.   mBio

High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy

(2015) Hyo Jung Lee et al.   Frontiers in Microbiology

Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage

(2015) Björn Breidenbach et al.   Frontiers in Microbiology

Meta-omics approaches to understand and improve wastewater treatment systems

(2015) Elisa Rodríguez et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

An overview of global rice production, supply, trade, and consumption

(2014) Sumithra Muthayya et al.   Annals of the New York Academy of Sciences

Response of a Rice Paddy Soil Methanogen to Syntrophic Growth as Revealed by Transcriptional Analyses

(2014) Pengfei Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Expanding the Verrucomicrobial Methanotrophic World: Description of Three Novel Species of Methylacidimicrobium gen. nov.

(2014) Muriel C. F. van Teeseling et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bloodstream infections due to Peptoniphilus spp.: report of 15 cases

(2014) K. Brown et al.   CLINICAL MICROBIOLOGY AND INFECTION

Evolution of bacterial communities in the wheat crop rhizosphere

(2014) Suzanne Donn et al.   ENVIRONMENTAL MICROBIOLOGY

Water addition regulates the metabolic activity of ammonia oxidizers responding to environmental perturbations in dry subhumid ecosystems

(2014) Hang-Wei Hu et al.   ENVIRONMENTAL MICROBIOLOGY

Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem

(2014) Hyo Jung Lee et al.   FEMS MICROBIOLOGY ECOLOGY

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

(2014) Baozhan Wang et al.   ISME Journal

Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate

(2014) Lingqin Leng et al.   MICROBIAL ECOLOGY

Methane fluxes show consistent temperature dependence across microbial to ecosystem scales

(2014) Gabriel Yvon-Durocher et al.   NATURE

The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

(2014) Federico M. Ibarbalz et al.   PLoS One

Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field

(2014) Akifumi Sugiyama et al.   PLoS One

Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

(2014) Shunsuke Takahashi et al.   PLoS One

Spatial Distribution and Factors Shaping the Niche Segregation of Ammonia-Oxidizing Microorganisms in the Qiantang River, China

(2013) Shuai Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane

(2013) Amelia-Elena Rotaru et al.   Energy & Environmental Science

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil

(2013) Xiubin Ke et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing

(2013) Ana R. Lopes et al.   FEMS MICROBIOLOGY ECOLOGY

Rhizosphere microbiome assemblage is affected by plant development

(2013) Jacqueline M Chaparro et al.   ISME Journal

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community structure of methanogenic archaea and methane production associated with compost-treated tropical rice-field soil

(2012) Alpana Singh et al.   FEMS MICROBIOLOGY ECOLOGY

Comparative genomic and physiological analysis provides insights into the role ofAcidobacteriain organic carbon utilization in Arctic tundra soils

(2012) Suman R. Rawat et al.   FEMS MICROBIOLOGY ECOLOGY

Acidobacterial community responses to agricultural management of soybean in Amazon forest soils

(2012) Acácio A. Navarrete et al.   FEMS MICROBIOLOGY ECOLOGY

Methanocella conradii sp. nov., a Thermophilic, Obligate Hydrogenotrophic Methanogen, Isolated from Chinese Rice Field Soil

(2012) Zhe Lü et al.   PLoS One

Metagenomic Analysis of a Southern Maritime Antarctic Soil

(2012) David A. Pearce et al.   Frontiers in Microbiology

Increased soil emissions of potent greenhouse gases under increased atmospheric CO2

(2011) Kees Jan van Groenigen et al.   NATURE

Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076

(2011) Jean F. Challacombe et al.   PLoS One

Functionalization of Methane in Anaerobic Microorganisms

(2010) Rudolf K. Thauer   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Influence of Plant Polymers on the Distribution and Cultivation of Bacteria in the PhylumAcidobacteria

(2010) Stephanie A. Eichorst et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Soil microbes drive the classic plant diversity–productivity pattern

(2010) Stefan A. Schnitzer et al.   ECOLOGY

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

(2010) Stéphane Uroz et al.   Environmental Microbiology Reports

Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils

(2009) N. L. Ward et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Nitrate and nitrite inhibition of methanogenesis during denitrification in granular biofilms and digested domestic sludges

(2009) Qais Banihani et al.   BIODEGRADATION

Bacteriarather thanArchaeadominate microbial ammonia oxidation in an agricultural soil

(2009) Zhongjun Jia et al.   ENVIRONMENTAL MICROBIOLOGY

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

TerraGenome: a consortium for the sequencing of a soil metagenome

(2009) Timothy M. Vogel et al.   NATURE REVIEWS MICROBIOLOGY

Environmental, genomic and taxonomic perspectives on methanotrophicVerrucomicrobia

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

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

(2008) Shaobin Hou et al.   Biology Direct

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Ammonia-oxidizing archaea: important players in paddy rhizosphere soil?

(2008) Xue-Ping Chen et al.   ENVIRONMENTAL MICROBIOLOGY

Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing

(2008) Matthias Noll et al.   FEMS MICROBIOLOGY ECOLOGY

Methane oxidation at 55 C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum

(2008) T. Islam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA