4.8 Article

Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Microbiology

Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts

Sunde Xu et al.

Summary: This study identified the bacterial microbiome associated with fungal fruiting bodies and discovered an effective bacterium, Pantoea agglomerans ZJU23, that suppresses fungal growth and infection. The study also identified a key antifungal compound, Herbicolin A, secreted by ZJU23, and determined its biosynthetic gene cluster. Herbicolin A demonstrated potent efficacy against various fungal pathogens both in vitro and in planta, and showed a distinct mode of action. Additionally, Herbicolin A exhibited higher activity against human opportunistic fungal pathogens than clinically used fungicides.

NATURE MICROBIOLOGY (2022)

Article Plant Sciences

Seed-borne, endospheric and rhizospheric core microbiota as predictors of plant functional traits across rice cultivars are dominated by deterministic processes

Junjie Guo et al.

Summary: Host-plant and microbiota mutually depend on each other, with the assembly of bacterial microbiota in different plant microhabitats shaped by deterministic processes. The presence of a core microbial community, consisting of generalist species, is key in connecting networks and predicting plant functional traits. This study enhances understanding of microbiota associations and driving mechanisms in plant microhabitats, offering new perspectives to enhance plant performance.

NEW PHYTOLOGIST (2021)

Article Microbiology

High level of conservation and diversity among the endophytic seed bacteriome in eight alpine grassland species growing at the Qinghai Tibetan Plateau

Danni Liang et al.

Summary: Seed borne microorganisms in native alpine grassland plants were characterized, revealing diverse bacterial populations with various functions. Plant species identity was found to be a key determinant shaping the seed bacterial community.

FEMS MICROBIOLOGY ECOLOGY (2021)

Review Microbiology

Microbial evolution and transitions along the parasite-mutualist continuum

Georgia C. Drew et al.

Summary: The review discusses different types of symbiotic interactions, including neutral, harmful, and beneficial effects, as well as the mechanisms and drivers of these evolutionary transitions. It also emphasizes the importance of understanding the dynamic life of microorganisms and how symbioses can impact the entire ecosystem.

NATURE REVIEWS MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

antiSMASH 6.0: improving cluster detection and comparison capabilities

Kai Blin et al.

Summary: antiSMASH, a tool for detecting biosynthetic gene clusters in microorganisms, has been updated to version 6, which increases the supported cluster types, displays the structure of multi-modular BGCs, adds a new comparison algorithm, allows integration of results from other prediction tools, and improves detection of tailoring enzymes in RiPP clusters.

NUCLEIC ACIDS RESEARCH (2021)

Letter Biochemistry & Molecular Biology

EVenn: Easy to create repeatable and editable Venn diagrams and Venn networks online

Tong Chen et al.

JOURNAL OF GENETICS AND GENOMICS (2021)

Article Biochemistry & Molecular Biology

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Michael Y. Galperin et al.

Summary: The COG database, created in 1997 and most recently updated in 2014, includes extensive information on bacterial and archaeal genomes. The current version introduces new features and plans for future expansion and refinement of annotations.

NUCLEIC ACIDS RESEARCH (2021)

Article Plant Sciences

Bacterial seed endophyte shapes disease resistance in rice

Haruna Matsumoto et al.

Summary: The study revealed that the endophyte bacterium Sphingomonas melonis can provide disease resistance to rice by producing anthranilic acid, inhibiting the virulence factor synthesis of the seed-borne pathogen Burkholderia plantarii. This finding offers new insights to combat globally widespread bacterial diseases threatening modern crop cultivation.

NATURE PLANTS (2021)

Article Biochemical Research Methods

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

Jasmine Chong et al.

NATURE PROTOCOLS (2020)

Review Microbiology

Xanthomonas diversity, virulence and plant-pathogen interactions

Sujan Timilsina et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Review Microbiology

Plant-microbiome interactions: from community assembly to plant health

Pankaj Trivedi et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Article Microbiology

Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds

Mengying Wang et al.

FRONTIERS IN MICROBIOLOGY (2020)

Article Microbiology

Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition

Adriana Parada Dias da Silveira et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2019)

Review Microbiology

Ecology and Evolution of Plant Microbiomes

Viviane Cordovez et al.

ANNUAL REVIEW OF MICROBIOLOGY, VOL 73 (2019)

Article Biotechnology & Applied Microbiology

NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

Jingying Zhang et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Ivica Letunic et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Environmental Sciences

Inheritance of seed and rhizosphere microbial communities through plant-soil feedback and soil memory

Hyun Gi Kong et al.

ENVIRONMENTAL MICROBIOLOGY REPORTS (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Article Plant Sciences

Identification and Characterization of the Core Rice Seed Microbiome

Alexander W. Eyre et al.

PHYTOBIOMES JOURNAL (2019)

Review Agronomy

The seed microbiome: Origins, interactions, and impacts

Eric B. Nelson

PLANT AND SOIL (2018)

Article Ecology

Saving seed microbiomes

Gabriele Berg et al.

ISME JOURNAL (2018)

Review Microbiology

Microbial interactions within the plant holobiont

M. Amine Hassani et al.

MICROBIOME (2018)

Article Microbiology

A microorganisms' journey between plant generations

Nathan Vannier et al.

MICROBIOME (2018)

Editorial Material Biotechnology & Applied Microbiology

The potential of plant microbiota in reducing postharvest food loss

Franziska Buchholz et al.

MICROBIAL BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

Article Microbiology

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

Seok-Hwan Yoon et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2017)

Article Biochemistry & Molecular Biology

Biodiversity and species competition regulate the resilience of microbial biofilm community

Kai Feng et al.

MOLECULAR ECOLOGY (2017)

Review Microbiology

Transmission of Bacterial Endophytes

Anna Carolin Frank et al.

MICROORGANISMS (2017)

Review Microbiology

Ecological patterns of seed microbiome diversity, transmission, and assembly

Ashley Shade et al.

CURRENT OPINION IN MICROBIOLOGY (2017)

Article Biotechnology & Applied Microbiology

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

Marcela Hernandez et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)

Review Microbiology

Microbiota and Host Nutrition across Plant and Animal Kingdoms

Stephane Hacquard et al.

CELL HOST & MICROBE (2015)

Review Plant Sciences

The importance of the microbiome of the plant holobiont

Philippe Vandenkoornhuyse et al.

NEW PHYTOLOGIST (2015)

Article Biochemistry & Molecular Biology

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

Seth R. Bordenstein et al.

PLOS BIOLOGY (2015)

Article Biotechnology & Applied Microbiology

Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water

Min Sun et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2015)

Review Environmental Sciences

Bacterial seed endophytes: genera, vertical transmission and interaction with plants

Sascha Truyens et al.

ENVIRONMENTAL MICROBIOLOGY REPORTS (2015)

Review Microbiology

Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae

Alyssa M. Walterson et al.

FEMS MICROBIOLOGY REVIEWS (2015)

Article Biochemical Research Methods

circlize implements and enhances circular visualization in R

Zuguang Gu et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

PanGP: A tool for quickly analyzing bacterial pan-genome profile

Yongbing Zhao et al.

BIOINFORMATICS (2014)

Review Ecology

Implications of streamlining theory for microbial ecology

Stephen J. Giovannoni et al.

ISME JOURNAL (2014)

Review Genetics & Heredity

Microbial genome-enabled insights into plant-microorganism interactions

David S. Guttman et al.

NATURE REVIEWS GENETICS (2014)

Article Multidisciplinary Sciences

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

Steven W. Kembel et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Review Plant Sciences

Diversity and Natural Functions of Antibiotics Produced by Beneficial and Plant Pathogenic Bacteria

Jos M. Raaijmakers et al.

ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 50 (2012)

Article Biochemical Research Methods

Molecular ecological network analyses

Ye Deng et al.

BMC BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis

A. Sessitsch et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2012)

Review Plant Sciences

Living inside plants: bacterial endophytes

Barbara Reinhold-Hurek et al.

CURRENT OPINION IN PLANT BIOLOGY (2011)

Article Multidisciplinary Sciences

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

Rodrigo Mendes et al.

SCIENCE (2011)

Article Biochemical Research Methods

A PCR-based toolbox for the culture-independent quantification of total bacterial abundances in plant environments

Gurdeep Rastogi et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2010)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Morgan N. Price et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Review Plant Sciences

Pantoea ananatis: an unconventional plant pathogen

Teresa A. Coutinho et al.

MOLECULAR PLANT PATHOLOGY (2009)

Review Plant Sciences

The type III effectors of Xanthomonas

Frank F. White et al.

MOLECULAR PLANT PATHOLOGY (2009)

Article Biotechnology & Applied Microbiology

Rice Seeds as Sources of Endophytic Bacteria

Hiroko Kaga et al.

MICROBES AND ENVIRONMENTS (2009)

Review Biotechnology & Applied Microbiology

Exploiting plant-microbe partnerships to improve biomass production and remediation

Nele Weyens et al.

TRENDS IN BIOTECHNOLOGY (2009)

Review Microbiology

Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution

Ilana Zilber-Rosenberg et al.

FEMS MICROBIOLOGY REVIEWS (2008)

Article Biotechnology & Applied Microbiology

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

Qiong Wang et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Review Biochemistry & Molecular Biology

Signals and Responses Choreographing the Complex Interaction between Legumes and alpha- and beta-Rhizobia

Angie Lee et al.

PLANT SIGNALING & BEHAVIOR (2006)

Review Plant Sciences

Xanthomonas oryzae pathovars: model pathogens of a model crop

David O. Nino-Liu et al.

MOLECULAR PLANT PATHOLOGY (2006)

Article Biochemistry & Molecular Biology

Infection and colonization of rice seedlings by the plant growth-promoting bacterium Herbaspirillum seropedicae Z67

EK James et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2002)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)