Assessment of endophytic bacterial diversity in rose by high-throughput sequencing analysis

Xia, Ao-Nan; Li, Jun; Kang, Dacheng; Zhang, Hai-Guang; Zhang, Ruhua; Liu, Yunguo

doi:10.1371/journal.pone.0230924

Cited by 16 publications

(5 citation statements)

References 41 publications

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“…These discrepancies may be attributed to variances in production techniques, fermentation conditions, and microbes present in rose. Xia et al (2020) employed throughput sequencing of 16S rDNA to reveal substantial differences in bacterial diversity across various regions where roses were grown. In a study conducted by Ramos et al (2020), next‐generation sequencing was utilized to analyze the impact of three different concentrations of cupuassu pulp fermentation (0%, 7.5%, and 15%) on microbial diversity (Ramos et al, 2020).…”

Section: Resultsmentioning

confidence: 99%

Microbial diversity and prediction function profiling of microbial communities in rose jam

Liu,

Xia,

Tang

et al. 2024

Journal of Food Safety

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The microbial diversity of rose jam was analyzed by high‐throughput sequencing, along with functional prediction of the bacterial community. The results indicate that Pseudomonas, Pantoea, and Burkholderia emerged were the top three dominant bacterial groups. Proteobacteria was particularly abundant in R4 (99.1%) and R6 (96.12%). Zygosaccharomyces, unclassified fungi, and Botrytis constituted the top three fungal groups. The presence of unclassified OTUs was observed in all samples, particularly in R6 (52.36%), R8 (45.28), and R9 samples (39.57%). Gene prediction using PICRUSt revealed the existence of multiple KEGG functional modules associated with human metabolism in each rose jam sample. The presence of a high abundance of functional genes indicated the microbial community's diverse wide range of microgenetic resources that can be further explored for research purposes. The microbial community found in rose jam exhibits remarkable diversity and encompasses valuable functional information relevant to human health.

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Section: Resultsmentioning

confidence: 99%

Microbial diversity and prediction function profiling of microbial communities in rose jam

Liu,

Xia,

Tang

et al. 2024

Journal of Food Safety

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“…For instance, the microbiome of Rosa spp. consists of bacteria, such as Bacillus and Staphylococcus (Xia et al, 2020), as well as fungi (Zhao et al, 2018). Furthermore, hyperproduction of peroxidase in the young D. rosae larvae may be regarded as a response to the defensive mechanisms of the host plant.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis ofDiplolepis rosae: revealing overexpression of genes potentially associated with insect immune response and gall formation at early larval stages

Mozhaitseva¹,

Tourrain¹,

Branca¹

2023

Preprint

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Insect parasites can provoke drastic changes in host plant physiology by affecting cell differentiation pathways and various metabolic processes. An intriguing example of such interaction is a gall, a novel outgrowing plant organ, induced by another organism for its own benefit. Cynipidae is a family of gall-inducing hymenopterans that induce galls with a complex anatomical structure. Gall formation involves three stages: initiation, growth, and maturation. Until today, the mechanism of gall initiation remains unknown. In this study, we aimed to reveal candidate genes involved in gall induction inDiplolepis rosae, a gall wasp inducing bedeguars in wild roses. We performed differential expression analysis of the gall wasp larva transcriptome. We observed the overexpression of genes encoding plant cell wall degrading enzymes. These enzymes may contribute to the formation of a chamber for a developing larva by lysing plant tissues. We also demonstrated the overexpression of genes encoding podocan, vasorin-like protein, toll-like receptor 7, tetraspanin, lipase, peroxidase, phospholipase A2, and venom acid phosphatase. These genes may be involved in insect development and the immune response against parasitoids, host plant microbiome, and host plant defense systems. Additionally, we performed a test for selection to detectD. rosaegenes under positive selection. However, we detected only one gene encoding a transposable element. This can be explained by the mostly asexual reproductive mode of this species. Thus, our study contributes to understanding the processes occurring in cynipid wasps during gall formation and creates opportunities for further investigations of other candidate genes.

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“…PICRUSt function prediction found that carbohydrate metabolism and energy metabolism functional genes were abundant in endophytic fungi in ordinary A. sinensis and Qi-Nan. Genes relevant to metabolism can influence plant growth, and beneficial microbes can synthesize and secrete secondary bioactive metabolites that maintain host plant health [70]; the endophytic fungi of Qi-Nan and ordinary A. sinensis perform such functions. In addition, studies have demonstrated that the process of agarwood formation involves carbohydrate metabolism in order to produce secondary metabolites.…”

Section: Endophytic Fungi Of Grafting Seedlingsmentioning

confidence: 99%

Physiological and Endophytic Fungi Changes in Grafting Seedlings of Qi-Nan Clones (Aquilaria sinensis)

Fang,

Li,

Zhang

et al. 2024

Forests

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In recent years, some new Qi-Nan clones of Aquilaria sinensis, which have the characteristics of easily induced and high-quality agarwood, have been selected and propagated by grafting seedlings. To date, research on the grafting of Qi-Nan seedlings is limited. In this study, the effects of grafting on physiological characteristics and endophytic fungi of seedlings within a short period after grafting were studied by means of histochemical observations, physiological index determinations and Illumina sequencing. The results showed that the grafting healing time of ordinary A. sinensis was at least 10 days shorter than that of Qi-Nan, according to the degree of lignification of callus, and the tissue basis for the healing was the interxylary phloem. The MDA content of Qi-Nan peaked earlier than that of ordinary A. sinensis. The contents of JA and ABA peaked earlier in ordinary A. sinensis, and the SA content was significantly higher than that of Qi-Nan at 20–40 days; on average, it was 17.33% higher than that of Qi-Nan. A total of 5 phyla, 28 classes, 84 orders, 197 families, 489 genera and 842 species of endophytic fungi were identified before and after grafting. After grafting, the abundance and diversity of endophytic fungi in ordinary A. sinensis and Qi-Nan decreased, and the endophytic fungi were significantly different before and after grafting. In ordinary A. sinensis, before grafting, Dothideomycetes was the dominant class, and after grafting, Sordariomycetes was the dominant class. The dominant class of Qi-Nan before and after grafting was Dothideomycetes. The dominant genus of ordinary A. sinensis before grafting was Devriesia, and after grafting, it was Fusarium; that of Qi-Nan before grafting was Hyweljonesia and after grafting was Arthopyrenia. Functional genes of the endophytic fungi were mostly related to carbohydrate metabolism and energy metabolism, which may be the reason why endophytic fungi promote agarwood formation in Aquilaria trees. The findings suggest that the healing of the grafting interface in A. sinensis seedlings was the result of multiple factors, and endophytic fungi of Qi-Nan scion changed after grafting.

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Assessment of endophytic bacterial diversity in rose by high-throughput sequencing analysis

Cited by 16 publications

References 41 publications

Microbial diversity and prediction function profiling of microbial communities in rose jam

Microbial diversity and prediction function profiling of microbial communities in rose jam

Transcriptome analysis ofDiplolepis rosae: revealing overexpression of genes potentially associated with insect immune response and gall formation at early larval stages

Physiological and Endophytic Fungi Changes in Grafting Seedlings of Qi-Nan Clones (Aquilaria sinensis)

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