Microbiomes inhabiting rice roots and rhizosphere

Ding, Long-Jun; Cui, Huiling; Nie, Shuang; Long, Xiaojing; Duan, Guilan; Zhu, Yan

doi:10.1093/femsec/fiz040

Cited by 129 publications

(80 citation statements)

References 160 publications

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“…In other model plants, both bacteria and fungi have been robustly detected in endospheres of plant organs, while the plants we examined were extreme in that we did not detect bacteria in endospheres of all their organs. Second, composition patterns of bacterial and fungal communities detected in the R. stylosa rhizosphere compartment differed from those of model plants reported in previous studies [10,[69][70][71][72]. Generally, Proteobacteria, Acidobacteria, Actinobacteria form the backbone of the bacterial rhizosphere microbiomes in the model plants.…”

Section: Comparison Of the R Stylosa Microbiome To Those Of Other Momentioning

confidence: 57%

“…Thus, the final goal of our work was to use R. stylosa as a model plant to investigate its microbiome and compare it to other model plants in other ecosystems [67], including: the general model plant Arabidopsis thaliana [68,69]; the model crop plants Oryza spp. (rice) [70,71] and Zea mays (maize) [72]; and the model forest tree genus Populus [10]. Overall, we found that the microbial communities of soil and plant compartments of R. stylosa had both unique and shared features with the other model plants.…”

Section: Comparison Of the R Stylosa Microbiome To Those Of Other Momentioning

confidence: 80%

“…In some specific soil types and locations, these two bacterial phyla also reportedly co-dominate the rhizosphere of Oryza spp. [70,71]. Third, Dikarya (Ascomycota and Basidiomycota) were the only fungi detected in the rhizosphere and endospheres (root, stem and leaf) of R. stylosa, while other, lower fungi, such as Zygomycota and Chytridiomycota, etc.…”

Section: Comparison Of the R Stylosa Microbiome To Those Of Other Momentioning

confidence: 99%

“…and Oryza spp., lower fungi of the Zygomycota even co-dominate the rhizosphere and/or root (in Populus spp.) microbiomes [10,71]. Locations, soil types, and environmental factors also strongly affect the taxonomic composition of bacterial and fungal communities at coarse and fine taxonomic resolutions in these model plants [69,70,[72][73][74].…”

Section: Comparison Of the R Stylosa Microbiome To Those Of Other Momentioning

confidence: 99%

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First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments

et al. 2019

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Mangrove forest trees play important ecological functions at the interface between terrestrial and marine ecosystems. However, despite playing crucial roles in plant health and productivity, there is little information on microbiomes of the tree species in mangrove ecosystems. Thus, in this study we aimed to characterize the microbiome in soil (rhizosphere) and plant (root, stem, and leaf endosphere) compartments of the widely distributed mangrove tree Rhizophora stylosa. Surprisingly, bacterial operational taxonomic units (OTUs) were only confidently detected in rhizosphere soil, while fungal OTUs were detected in all soil and plant compartments. The major detected bacterial phyla were affiliated to Proteobacteria, Actinobacteria, Planctomycetes, and Chloroflexi. Several nitrogen-fixing bacterial OTUs were detected, and the presence of nitrogen-fixing bacteria was confirmed by nifH gene based-PCR in all rhizosphere soil samples, indicating their involvement in N acquisition in the focal mangrove ecosystem. We detected taxonomically (54 families, 83 genera) and functionally diverse fungi in the R. stylosa mycobiome. Ascomycota (mainly Dothideomycetes, Eurotiomycetes, Sordariomycetes) were most diverse in the mycobiome, accounting for 86% of total detected fungal OTUs. We found significant differences in fungal taxonomic and functional community composition among the soil and plant compartments. We also detected significant differences in fungal OTU richness (p < 0.002) and community composition (p < 0.001) among plant compartments. The results provide the first information on the microbiome of rhizosphere soil to leaf compartments of mangrove trees and associated indications of ecological functions in mangrove ecosystems.

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Section: Comparison Of the R Stylosa Microbiome To Those Of Other Momentioning

confidence: 57%

Section: Comparison Of the R Stylosa Microbiome To Those Of Other Momentioning

confidence: 80%

Section: Comparison Of the R Stylosa Microbiome To Those Of Other Momentioning

confidence: 99%

Section: Comparison Of the R Stylosa Microbiome To Those Of Other Momentioning

confidence: 99%

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First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments

et al. 2019

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“…Sane and Mehta (2015) showed that phosphate solubilizing bacteria and fungi in co-inoculation increase the mobilization of rock phosphate and plant growth. Authors Zaidi et al (2017) and Ding et al (2019) reported that PSMs isolated from the rice rhizosphere released 22-826 µg P mL −1 in in vitro test. Among the PSMs, Actinobacteria (Actinomyces) are of special interest since these filamentous sporulating bacteria (see details in Box 2) are able to develop in extremely different soils and offering a unique opportunity for biotechnological application (Mengual et al, 2016).…”

Section: Potential Features Of Phosphate Solubilizing Actinobacteriamentioning

confidence: 99%

From Isolation of Phosphate Solubilizing Microbes to Their Formulation and Use as Biofertilizers: Status and Needs

Soumaré

Boubekri

Lyamlouli

et al. 2020

Front. Bioeng. Biotechnol.

130

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The production of biofertilizers at industrial level is a bottleneck because bacterial strains are generally developed and managed by research laboratories and not by production units. A seamless transition from laboratory to field application is, therefore necessary. This review provides an overview of the constraints that limiting the application or the implementation of Actinobacteria based biofertilizers especially in agricultural field and suggests solutions to overcome some of these limits. General processes of making and controlling the quality of the inoculum are briefly described. In addition, the paper underlines the opportunity of biofertilizers alone or in combination with chemical fertilizers. This review also, highlights the latest studies (until June 2019) and focuses on P-solubilization microorganisms mainly Actinobacteria. The biotechnology of these bacteria is a glimmer of hope for rock phosphate (RP) bioformulation. Since direct application of RP fertilizer is not always agronomically effective due to its sparse solubility.

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Rice Growth in the Shadow of Global Warming: Microbes Shed Light on Alleviating Its Heat Stress

Zeng,

Wang,

et al. 2024

J of Sust Agri & Env

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The increasing severity of global climate change has led to more frequent extreme high‐temperature events, significantly damaging rice yield and quality, thus posing a threat to global food security. Research indicates that plant‐microbe interactions can enhance plant growth and overall health under adverse conditions. Therefore, this review aims to explore strategies to improve rice heat tolerance through thermophilic microorganism mediation. This paper systematically summarises the effects of heat stress on both the aboveground and underground parts of rice during its growth stages, identifies the molecular mechanisms by which rice responds to heat stress, and explores the potential roles of microorganisms. Additionally, we review existing studies on microorganisms that alleviate plant heat stress and their mechanisms of action. Through case studies, we explore how microorganisms enhance rice survival in high‐temperature environments by regulating its growth and development, along with their potential applications in sustainable agriculture. In the future, environmentally friendly and efficient microbial inoculants and biofertilizers are expected to be developed based on microbe‐mediated plant heat tolerance mechanisms, which will help mitigate the heat stress challenges crops face under global climate change.

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Microbiomes inhabiting rice roots and rhizosphere

Cited by 129 publications

References 160 publications

First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments

First Insights into the Microbiome of a Mangrove Tree Reveal Significant Differences in Taxonomic and Functional Composition among Plant and Soil Compartments

From Isolation of Phosphate Solubilizing Microbes to Their Formulation and Use as Biofertilizers: Status and Needs

Rice Growth in the Shadow of Global Warming: Microbes Shed Light on Alleviating Its Heat Stress

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