Succession of Composition and Function of Soil Bacterial Communities During Key Rice Growth Stages

Changes in soil microbial community and organic carbon fractions under short-term straw return in a rice–wheat cropping system

(2017) Zhaoming Chen et al.   SOIL & TILLAGE RESEARCH

Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations

(2017) Fang Li et al.   Frontiers in Microbiology

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

(2017) Yi Yang et al.   PLoS One

Temporal variation of diazotrophic community abundance and structure in surface and subsoil under four fertilization regimes during a wheat growing season

(2016) Jichen Wang et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Responses of soil properties and crop yields to different inorganic and organic amendments in a Swiss conventional farming system

(2016) Guillaume Blanchet et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Effect of 35 years inorganic fertilizer and manure amendment on structure of bacterial and archaeal communities in black soil of northeast China

(2016) Jianli Ding et al.   APPLIED SOIL ECOLOGY

Effects of organic–inorganic compound fertilizer with reduced chemical fertilizer application on crop yields, soil biological activity and bacterial community structure in a rice–wheat cropping system

(2016) Jun Zhao et al.   APPLIED SOIL ECOLOGY

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

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Shifts in microbial communities do not explain the response of grassland ecosystem function to plant functional composition and rainfall change

(2016) Ellen L. Fry et al.   SOIL BIOLOGY & BIOCHEMISTRY

The phenological stage of rice growth determines anaerobic ammonium oxidation activity in rhizosphere soil

(2016) Hu Li et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

(2016) Jichen Wang et al.   Frontiers in Microbiology

Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River

(2016) Wenhui Wang et al.   Scientific Reports

Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity

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

Soil microbial community structure and function relationships: A heat stress experiment

(2015) Wassila Riah-Anglet et al.   APPLIED SOIL ECOLOGY

Consistent increase in abundance and diversity but variable change in community composition of bacteria in topsoil of rice paddy under short term biochar treatment across three sites from South China

(2015) Junhui Chen et al.   APPLIED SOIL ECOLOGY

Changes in soil microbial community structure and functional diversity in the rhizosphere surrounding mulberry subjected to long-term fertilization

(2015) C. Yu et al.   APPLIED SOIL ECOLOGY

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

Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw

(2015) Ruibo Sun et al.   SOIL BIOLOGY & BIOCHEMISTRY

Roots from distinct plant developmental stages are capable of rapidly selecting their own microbiome without the influence of environmental and soil edaphic factors

(2015) Jun Yuan et al.   SOIL BIOLOGY & BIOCHEMISTRY

Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China

(2015) Jing Zhou et al.   SOIL BIOLOGY & BIOCHEMISTRY

Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead?

(2015) Aimée T. Classen et al.   Ecosphere

Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing

(2015) Hongmei Jing et al.   Frontiers in Microbiology

Biochar does not affect soil N-transformations or microbial community structure under ruminant urine patches but does alter relative proportions of nitrogen cycling bacteria

(2014) C.R. Anderson et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Effects of bio-organic fertilizer plus soil amendment on the control of tobacco bacterial wilt and composition of soil bacterial communities

(2014) Kai Wu et al.   BIOLOGY AND FERTILITY OF SOILS

Rhizosphere interactions: root exudates, microbes, and microbial communities

(2014) Xing-Feng Huang et al.   Botany

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

(2014) Francisco Dini-Andreote et al.   ISME Journal

High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation

(2014) Dawei Ren et al.   ISME Journal

High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model

(2014) Jun Ma et al.   Nature Communications

A Field Study on Effects of Nitrogen Fertilization Modes on Nutrient Uptake, Crop Yield and Soil Biological Properties in Rice-Wheat Rotation System

(2013) Guan GUAN et al.   Agricultural Sciences in China

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Quantitatively Different, yet Qualitatively Alike: A Meta-Analysis of the Mouse Core Gut Microbiome with a View towards the Human Gut Microbiome

(2013) Lukasz Krych et al.   PLoS One

Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes

(2013) Emily B. Graham et al.   SOIL BIOLOGY & BIOCHEMISTRY

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA

(2012) Emily L Kara et al.   ISME Journal

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

(2011) J. Zhou et al.   mBio

Succession of methanotrophs in oxygen–methane counter-gradients of flooded rice paddies

(2010) Sascha Krause et al.   ISME Journal

Functional Molecular Ecological Networks

(2010) J. Zhou et al.   mBio

Succession of Bacterial Populations during Plant Residue Decomposition in Rice Field Soil

(2009) J. Rui et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY