Structural variability and differentiation of niches in the rhizosphere and endosphere bacterial microbiome of moso bamboo (Phyllostachys edulis)

Yuan, Zong-Sheng; Liu, Fang; Liu, Zhenyu; Huang, Qiuliang; Zhang, Guofang; Pan, Hui

doi:10.1038/s41598-021-80971-9

Cited by 23 publications

(19 citation statements)

References 50 publications

(31 reference statements)

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“… 63–65 Other predicted functions involved indole-3-acetic acid and siderophore production, antibiotic synthesis, and phosphate solubilization may enhance plant growth and health through nitrogen fixation, root development, the bioavailability of soil nutrients for plant uptake, and synthesis of biocontrol agent against phytopathogens. 66 In line with this study, the predicted functional analysis of endophytic bacteria associated with sunflower root and stem corroborate the findings of 67 , who reported similar potential functions exhibited by endophytic bacteria associated with flowering and nonflowering moso bamboo ( Phyllostachys edulis ). The predicted functional reports on endophytic bacteria colonizing the sunflower endosphere have not been documented.…”

Section: Discussionsupporting

confidence: 89%

Bacterial community structure of the sunflower (Helianthus annuus) endosphere

Adeleke

Babalola

2021

Plant Signaling & Behavior

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Agrochemical applications on farmland aim to enhance crop yield; however, the consequence of biodiversity loss has caused a reduction in ecological functions. The positive endosphere interactions and crop rotation systems may function in restoring a stable ecosystem. Employing culture-independent techniques will help access the total bacteria community in the sunflower endosphere. Limited information is available on the bacteria diversity in sunflower plants cultivated under different agricultural practices. Hence, this study was designed to investigate the endophytic bacterial community structure of sunflower at the growing stage. Plant root and stem samples were sourced from two locations (Itsoseng and Lichtenburg), for DNA extraction and sequenced on the Illumina Miseq platform. The sequence dataset was analyzed using online bioinformatics tools. Saccharibacteria and Acidobacteria were dominant in plant roots, while the stem is dominated by Proteobacteria, Bacteriodetes, and Gemmatimonadetes across the sites. Bacterial genera, Acidovorax, Flavobacterium, Hydrogenophaga , and Burkholderia-Paraburkhoderia were found dominant in the root, while the stem is dominated by Streptomyces . The diverse bacterial community structure at phyla and class levels were significantly different in plant organs across the sites. The influence of soil physical and chemical parameters analyzed was observed to induce bacterial distribution across the sites. This study provides information on the dominant bacteria community structure in sunflowers at the growing stage and their predictive functions, which suggest their future exploration as bioinoculants for improved agricultural yields.

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Section: Discussionsupporting

confidence: 89%

Bacterial community structure of the sunflower (Helianthus annuus) endosphere

Adeleke

Babalola

2021

Plant Signaling & Behavior

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“…In addition, the proportion of Acidobacteria in rhizosphere soil (12.71%) was significantly higher than that in the nodules (0.74%) and the bulk soil (3.76%), and this finding was consistent with previous reports in many plants and soils (Bulgarelli et al, 2012;Chen et al, 2019;Lin et al, 2019). In the present study, Proteobacteria were absolutely dominant within the root nodules, which may be the result of the differentiation of specific bacteria within different niches and the active filtration of bacteria by the host plants (Bulgarelli et al, 2013;Yuan et al, 2021). This might be because Proteobacteria thrive better under high nutrient conditions (Zhao et al, 2017) and tend to exploit more labile C sources (Fierer et al, 2007).…”

Section: Discussionsupporting

confidence: 93%

Environmental filtering drives the establishment of the distinctive rhizosphere, bulk, and root nodule bacterial communities of Sophora davidii in hilly and gully regions of the Loess Plateau of China

Liu

et al. 2022

Front. Microbiol.

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In addition to the rhizobia, other non-rhizobial endophytes (NREs) have been simultaneously isolated from the root nodules. The existence of NREs in leguminous root nodules is a universal phenomenon, and they have the potential to enhance legume survival, especially under conditions of environmental stress. However, the diversity and biogeographic patterns of microbial communities inhabiting root nodules are not well studied or understood. Here, we explored and characterized the diversity of NRE bacteria by using 16S rRNA gene high-throughput amplicon sequencing. Additionally, we compared the biogeography and co-occurrence patterns in review of the bacterial microbiota inhabiting the rhizosphere, the bulk soil and the root nodule bacterial communities associated with Sophora davidii, a native N-fixing wild leguminous shrub in hilly and gully regions of the Loess Plateau of China. The results showed the presence of a large diversity of bacteria belonging to 81 phyla, 154 classes, 333 orders, 463 families, and 732 genera inside the nodules. Proteobacteria were dominant in the nodule and rhizosphere soil samples, and Actinomycetes were dominant in the bulk soil samples. Mesorhizobium was the dominant genus in the nodules, accounting for between 60.15 and 83.74% of the bacteria. The microbial community composition of the NRE in the root nodules differed from that in the rhizosphere soil and the bulk soil of S. davidii. Moreover, we found that the biogeographic patterns and assembly process of the rhizobia and non-rhizobia communities differed in the root nodule, the rhizosphere soil and the bulk soil. Furthermore, the correlation analysis between the soil’s physical and chemical properties and the bacteria showed that available phosphorus was the predominant factor affecting the bacterial diversity within the rhizosphere soil. Finally, our results revealed that the microbial network diagram of co-occurrence patterns showed more complexes in the soil than in the root nodules. This indicates that only specific microorganisms could colonize and thrive in the rhizosphere through the selection and filtering effects of roots. In conclusion, there are significant differences in bacterial community composition in the nodules, rhizosphere and bulk soil in the hilly and gully region of the Loess Plateau, which is the result of environmental filtration. Our study improves the understanding of the biogeographic patterns and diversity of bacterial microbiota inhabiting root nodules and can help quantify and define the root nodule assemblage process of S. davidii.

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“…These bacteria are broadly split into two compartments, those surrounding the root surface (the rhizosphere) and those living inside the root (the endosphere). External inputs can cause changes in plant microbiome communities, which in turn may boost plant growth by controlling hormonal signaling, competing with pathogens, and increasing the bioavailability of nutrients ( 1 – 5 ). In particular, bacteria and fungi act to depolymerize and mineralize organic forms of N, P, and S, allowing for more efficient uptake by the plant ( 6 – 8 ).…”

Section: Introductionmentioning

confidence: 99%