Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project

Román-Reyna, Verónica; Pinili, Dale; Borja, Frances Nikki; Quibod, Ian Lorenzo; Groen, Simon C.; Alexandrov, Nickolai N.; Mauleon, Ramil; Oliva, Ricardo

doi:10.1186/s12284-020-00432-1

Cited by 36 publications

(11 citation statements)

References 49 publications

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“…Root microbiome of C. myrtifolia contained Actinobacteria, Proteobacteria, Firmicutes, Cyanobacteria, Bacteroidetes , and others, which is very similar to composition of Alnus glutinosa root microbiome ( Thiem et al, 2018 ), Casuarina glauca ( Ghodhbane-Gtari et al, 2021 ), several Legume roots ( Miranda-Sánchez et al, 2016 ; Xiao et al, 2017 ; Zgadzaj et al, 2016 ), and rice ( Edwards et al, 2015 ; Roman-Reyna et al, 2020 ).…”

Section: Discussionmentioning

confidence: 75%

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

Swanson

Sbissi²,

Ktari³

et al. 2022

Front. Microbiol.

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The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.

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Section: Discussionmentioning

confidence: 75%

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

Swanson

Sbissi²,

Ktari³

et al. 2022

Front. Microbiol.

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“…Progress in cutting-edge next-generation sequencing, with decreased costs, have permitted to acquire plant genotype through single nucleotide polymorphisms (SNPs). In future, the data attained through shotgun metagenomics will promote mapping microbial functions, as recently conducted in the phyllosphere microbiome of rice [ 128 ].…”

Section: Omics Tools: Putative Role and Limitations In Plant Microbio...mentioning

confidence: 99%

Plant Microbiome Engineering: Hopes or Hypes

Afridi

Ali

Salam

et al. 2022

Biology

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Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant’s second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.

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“…As an open environment that is subject to diverse biotic stimuli, e.g., insect and pathogen invasions, the phyllosphere microbiome is composed of a mixture of commensal, beneficial, and pathogenic species [ 57 ]. Roman-Reyna et al [ 58 ] found that the microbial community composition on rice leaves could be delineated in terms of 12 genera that span a range from commensal or pathogenic to beneficial, e.g., Clostridium , Bacillus , Helicobacter , Azotobacter, and Pseudomonas.…”

Section: The Diverse and Dynamic Structures Of Rice Microbiomesmentioning

confidence: 99%

Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of ‘Omics’ Technologies

Doni

Suhaimi

Mispan

et al. 2022

IJMS

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Rice, the main staple food for about half of the world’s population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial–rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.

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Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project

Cited by 36 publications

References 49 publications

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere

Plant Microbiome Engineering: Hopes or Hypes

Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of ‘Omics’ Technologies

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