Comparative Metagenomic and Metabolomic Profiling of Rhizospheres of Panax notoginseng Grown under Forest and Field Conditions

Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages

(2021) Ai-Zi Tong et al.   BMC MICROBIOLOGY

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

(2021) Weibing Xun et al.   Microbiome

Metabolome and transcriptome analysis reveals the molecular profiles underlying the ginseng response to rusty root symptoms

(2021) Xingbo Bian et al.   BMC PLANT BIOLOGY

Use of untargeted metabolomics for assessing soil quality and microbial function

(2020) Emma Withers et al.   SOIL BIOLOGY & BIOCHEMISTRY

Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau

(2020) Mengjun Zhang et al.   BMC MICROBIOLOGY

Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms

(2020) Andika Sidar et al.   Frontiers in Bioengineering and Biotechnology

Influence of the carbohydrate-binding module on the activity of a fungal AA9 lytic polysaccharide monooxygenase on cellulosic substrates

(2019) Amani Chalak et al.   Biotechnology for Biofuels

Combining microdialysis with metabolomics to characterize the in situ composition of dissolved organic compounds in boreal forest soil

(2019) Dörte Randewig et al.   SOIL BIOLOGY & BIOCHEMISTRY

Metagenomic analysis of antibiotic resistance genes in coastal industrial mariculture systems

(2018) Jian-Hua Wang et al.   BIORESOURCE TECHNOLOGY

Archaea Are Interactive Components of Complex Microbiomes

(2018) Christine Moissl-Eichinger et al.   TRENDS IN MICROBIOLOGY

Roles of Plant-Associated Microbiota in Traditional Herbal Medicine

(2018) Weijuan Huang et al.   TRENDS IN PLANT SCIENCE

Rhizospheric microbial communities are driven by Panax ginseng at different growth stages and biocontrol bacteria alleviates replanting mortality

(2018) Linlin Dong et al.   Acta Pharmaceutica Sinica B

The Biogeographical Distribution of Soil Bacterial Communities in the Loess Plateau as Revealed by High-Throughput Sequencing

(2018) Dong Liu et al.   Frontiers in Microbiology

Rhizospheric soil and root endogenous fungal diversity and composition in response to continuous Panax notoginseng cropping practices

(2017) Yong Tan et al.   MICROBIOLOGICAL RESEARCH

Whole-Genome Sequencing and Analysis of the Chinese Herbal Plant Panax notoginseng

(2017) Wei Chen et al.   Molecular Plant

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests

(2017) Luis E. Castañeda et al.   PeerJ

Significant relationship between soil bacterial community structure and incidence of bacterial wilt disease under continuous cropping system

(2016) Siyuan She et al.   ARCHIVES OF MICROBIOLOGY

Improved Growth and Metabolite Accumulation in Codonopsis pilosula (Franch.) Nannf. by Inoculation of Bacillus amyloliquefaciens GB03

(2016) Qi Zhao et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Quality Assessment of Panax notoginseng from Different Regions through the Analysis of Marker Chemicals, Biological Potency and Ecological Factors

(2016) Hai-zhu Zhang et al.   PLoS One

Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng

(2016) Chunping Xiao et al.   Journal of Ginseng Research

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

(2016) Cristina N. Butterfield et al.   PeerJ

Soil bacterial and fungal community dynamics in relation to Panax notoginseng death rate in a continuous cropping system

(2016) Linlin Dong et al.   Scientific Reports

Soil Microbes Compete Strongly with Plants for Soil Inorganic and Amino Acid Nitrogen in a Semiarid Grassland Exposed to Elevated CO2 and Warming

(2015) Janet Chen et al.   ECOSYSTEMS

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

Environmental characteristics of Agulhas rings affect interocean plankton transport

(2015) E. Villar et al.   SCIENCE

Untargeted soil metabolomics methods for analysis of extractable organic matter

(2015) Tami L. Swenson et al.   SOIL BIOLOGY & BIOCHEMISTRY

Bacterial Diversity in the Rhizosphere of Cucumbers Grown in Soils Covering a Wide Range of Cucumber Cropping Histories and Environmental Conditions

(2014) Yongqiang Tian et al.   MICROBIAL ECOLOGY

Different Continuous Cropping Spans Significantly Affect Microbial Community Membership and Structure in a Vanilla-Grown Soil as Revealed by Deep Pyrosequencing

(2014) Wu Xiong et al.   MICROBIAL ECOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

(2013) Chengwei Luo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates

(2013) Vimalier Reyes-Ortiz et al.   Biotechnology for Biofuels

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The microbiome of medicinal plants: diversity and importance for plant growth, quality and health

(2013) Martina Köberl et al.   Frontiers in Microbiology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Symptomatic atherosclerosis is associated with an altered gut metagenome

(2012) Fredrik H. Karlsson et al.   Nature Communications

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Analysis of Bacterial Community in the Ginseng Soil Using Denaturing Gradient Gel Electrophoresis (DGGE)

(2011) Regupathy Thamizh Vendan et al.   INDIAN JOURNAL OF MICROBIOLOGY

The iron-oxidizing proteobacteria

(2011) S. Hedrich et al.   MICROBIOLOGY-SGM

Microbial Communities Associated with Potato Common Scab-Suppressive Soil Determined by Pyrosequencing Analyses

(2011) Noah Rosenzweig et al.   PLANT DISEASE

Access to cellulose limits the efficiency of enzymatic hydrolysis: the role of amorphogenesis

(2010) Valdeir Arantes et al.   Biotechnology for Biofuels

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Soil Microbial Community Responses to Multiple Experimental Climate Change Drivers

(2009) H. F. Castro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A New Species of Panax L. (Araliaceae) from Sikkim Himalaya, India

(2009) Shiva Kumar Sharma et al.   SYSTEMATIC BOTANY

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

Plant host habitat and root exudates shape soil bacterial community structure

(2008) Feth el Zahar Haichar et al.   ISME Journal

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Do plant species with different growth strategies vary in their ability to compete with soil microbes for chemical forms of nitrogen?

(2007) Kathryn A. Harrison et al.   SOIL BIOLOGY & BIOCHEMISTRY

Differences in the composition and diversity of bacterial communities from agricultural and forest soils

(2007) Rima Upchurch et al.   SOIL BIOLOGY & BIOCHEMISTRY