Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication

Research Advances of Beneficial Microbiota Associated with Crop Plants

(2020) Lei Tian et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Powdered activated carbon facilitates methane productivity of anaerobic co-digestion via acidification alleviating: Microbial and metabolic insights

(2020) Jiaying Ma et al.   BIORESOURCE TECHNOLOGY

An evolving view of methane metabolism in the Archaea

(2019) Paul N. Evans et al.   NATURE REVIEWS MICROBIOLOGY

Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice

(2019) Lin Cheng et al.   Scientific Reports

Cultivated rice rhizomicrobiome is more sensitive to environmental shifts than that of wild rice in natural environments

(2019) Shangqi Xu et al.   APPLIED SOIL ECOLOGY

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia

(2019) Juan E. Pérez-Jaramillo et al.   Microbiome

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

(2019) Vanessa L. Brisson et al.   Scientific Reports

Community structures of the rhizomicrobiomes of cultivated and wild soybeans in their continuous cropping

(2019) Lei Tian et al.   MICROBIOLOGICAL RESEARCH

Chloroplast phylogeography of AA genome rice species

(2018) Ali Mohammad Moner et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

Co-evolutionary associations between root-associated microbiomes and root transcriptomes in wild and cultivated rice varieties

(2018) Lei Tian et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Comparative analysis of the root transcriptomes of cultivated and wild rice varieties in response to Magnaporthe oryzae infection revealed both common and species-specific pathogen responses

(2018) Lei Tian et al.   Rice

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice

(2018) Joseph A. Edwards et al.   PLOS BIOLOGY

Processes that determine the interplay of root exudation, methane emission and yield in rice agriculture

(2018) D. Maurer et al.   PLANT BIOLOGY

Impact of domestication on the evolution of rhizomicrobiome of rice in response to the presence of Magnaporthe oryzae

(2018) Shaohua Shi et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Limited potential of harvest index improvement to reduce methane emissions from rice paddies

(2018) Yu Jiang et al.   GLOBAL CHANGE BIOLOGY

Rice root morphological and physiological traits interaction with rhizosphere soil and its effect on methane emissions in paddy fields

(2018) Yun Chen et al.   SOIL BIOLOGY & BIOCHEMISTRY

Mechanism of plant mediated methane emission in tropical lowland rice

(2018) P. Bhattacharyya et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism

(2017) Christopher Staley et al.   Microbiome

Root-associated bacterial diversities of Oryza rufipogon and Oryza sativa and their influencing environmental factors

(2016) Lei Tian et al.   ARCHIVES OF MICROBIOLOGY

Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere

(2016) Yan Yan et al.   ISME Journal

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water

(2016) Xiao-Ming Lu et al.   MICROBIAL ECOLOGY

Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus

(2016) Jonathan W. Leff et al.   NEW PHYTOLOGIST

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

Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition

(2016) Matthew Shenton et al.   Rice

Greenhouse gas emissions intensity of global croplands

(2016) Kimberly M. Carlson et al.   Nature Climate Change

Flood and drought tolerance in rice: opposite but may coexist

(2016) A. N. M. Rubaiyath Bin Rahman et al.   Food and Energy Security

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

Cross-kingdom similarities in microbiome functions

(2015) Rodrigo Mendes et al.   ISME Journal

Metabolic engineering in methanotrophic bacteria

(2015) Marina G. Kalyuzhnaya et al.   METABOLIC ENGINEERING

Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice

(2015) J. Su et al.   NATURE

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Bacterial networks and co-occurrence relationships in the lettuce root microbiota

(2014) Massimiliano Cardinale et al.   ENVIRONMENTAL MICROBIOLOGY

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Methane-rich water induces cucumber adventitious rooting through heme oxygenase1/carbon monoxide and Ca2+ pathways

(2014) Weiti Cui et al.   PLANT CELL REPORTS

Influence of Soil Type, Cultivar and Verticillium dahliae on the Structure of the Root and Rhizosphere Soil Fungal Microbiome of Strawberry

(2014) Srivathsa Nallanchakravarthula et al.   PLoS One

Different behaviour of methanogenic archaea andThaumarchaeotain rice field microcosms

(2013) Xiubin Ke et al.   FEMS MICROBIOLOGY ECOLOGY

The Shikimate Pathway and Aromatic Amino Acid Biosynthesis in Plants

(2012) Hiroshi Maeda et al.   Annual Review of Plant Biology

Evolution of the African Rice: A Historical and Biological Perspective

(2012) N. M. Nayar   CROP SCIENCE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice

(2011) Daniel L. E. Waters et al.   Ecology and Evolution

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Activity and composition of the methanogenic archaeal community in soil vegetated with wild versus cultivated rice

(2009) Ralf Conrad et al.   SOIL BIOLOGY & BIOCHEMISTRY

Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea

(2008) Yuchen Liu et al.   Annals of the New York Academy of Sciences

Disruption of retinoid transport, metabolism and signaling by environmental pollutants

(2008) Jiří Novák et al.   ENVIRONMENT INTERNATIONAL