ArticleCommunications biology2024
Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing.
Article in Communications biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Plasmidomics: studying plasmids as ecological entities beyond their hosts.Microbial genomics · 2026Review
- Horizontal acquisition of nicotine catabolism gene cluster enhances Arthrobacter fitness within tobacco root microbiota.Microbiome · 2026Article
- Rice Genotype-Dependent Phyllosphere Microbiome Assembly and Isolation of AntagonisticInternational journal of molecular sciences · 2026Article
- Recent Microbial Evolutionary Insights From Metagenomics.Genome biology and evolution · 2026Review
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Metagenomic Tools as Predictive Approaches to Decipher Soil and Rhizosphere Microbial Communities and Their Functions for Sustainable Agriculture.International journal of genomics · 2026Review
- Phyllosphere microbiomes uncovered: Research trends, geographic disparities, and key microbial players.Genetics and molecular biology · 2026Article
- Species-level bacterial community shift in rice growth stages.Plant biotechnology (Tokyo, Japan) · 2025Article
- The Rice-Microbe Nexus: Unlocking Productivity Through Soil Science.Rice (New York, N.Y.) · 2025Review
- Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater.Microorganisms · 2025Article
- Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience.Microorganisms · 2025Review
- Expanding the Eco-collection of Methane-oxidizing Bacteria Inhabiting Rice Roots: Cultivation, Isolation, and Genomic Characterization of Isolates.Microbes and environments · 2025Article
- Roles of Phyllosphere Microbes in Rice Health and Productivity.Plants (Basel, Switzerland) · 2024Review
- Divergence and convergence in epiphytic and endophytic phyllosphere bacterial communities of rice landraces.mSphere · 2024Article
- Seeing in the dark: a metagenomic approach can illuminate the drivers of plant disease.Frontiers in plant science · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The plant microbiome is crucial for plant growth, yet many important questions remain, such as the identification of specific bacterial species in plants, their genetic content, and location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice-phyllosphere, we perform a metagenomic analysis using long-read sequences. Here, 1.8 Gb reads are assembled into 26,067 contigs including 142 circular sequences. Within these contigs, 669 complete 16S rRNA genes are clustered into 166 bacterial species, 121 of which show low identity (<97%) to defined sequences, suggesting novel species. The circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs are defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of a difficult-to-culture bacterium Candidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.
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