Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice ( Oryza sativa L.)

Wang, Wenfeng; Zhai, Yanyan; Cao, Lixue; Tan, Hongming; Zhang, Renduo

doi:10.1016/j.micres.2016.04.009

Cited by 111 publications

(58 citation statements)

References 39 publications

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“…Evolutionary evidence has suggested that many land plants establish symbiotic relations with diverse microbes, such as bacteria, fungi, and actinomycetes, all of which can dwell in their roots and other organs . Studies have established the beneficial aspects of plant‐microbes in terms of providing a shield against phyto‐pathogens while negating the ill effects of stresses .…”

Section: Mel Regulates Plant‐rhizomicrobial Interactionsmentioning

confidence: 99%

Phytomelatonin: Recent advances and future prospects

Kanwar

Zhou

2018

Journal of Pineal Research

175

109

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Melatonin (MEL) has been revealed as a phylogenetically conserved molecule with a ubiquitous distribution from primitive photosynthetic bacteria to higher plants, including algae and fungi. Since MEL is implicated in numerous plant developmental processes and stress responses, the exploration of its functions in plant has become a rapidly progressing field with the new paradigm of involvement in plants growth and development. The pleiotropic involvement of MEL in regulating the transcripts of numerous genes confirms its vital involvement as a multi‐regulatory molecule that architects many aspects of plant development. However, the cumulative research in plants is still preliminary and fragmentary in terms of its established functions compared to what is known about MEL physiology in animals. This supports the need for a comprehensive review that summarizes the new aspects pertaining to its functional role in photosynthesis, phytohormonal interactions under stress, cellular redox signaling, along with other regulatory roles in plant immunity, phytoremediation, and plant microbial interactions. The present review covers the latest advances on the mechanistic roles of phytomelatonin. While phytomelatonin is a sovereign plant growth regulator that can interact with the functions of other plant growth regulators or hormones, its qualifications as a complete phytohormone are still to be established. This review also showcases the yet to be identified potentials of phytomelatonin that will surely encourage the plant scientists to uncover new functional aspects of phytomelatonin in plant growth and development, subsequently improving its status as a potential new phytohormone.

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Section: Mel Regulates Plant‐rhizomicrobial Interactionsmentioning

confidence: 99%

Phytomelatonin: Recent advances and future prospects

Kanwar

Zhou

2018

Journal of Pineal Research

175

109

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show abstract

“…During their evolution, most land plants, developed symbiotic associations with microbes, including fungi, bacteria, and actinomycetes that can grow in the roots and other plant tissues (Compant et al, 2011; Hameed et al, 2015; Wang et al, 2016). Numerous plant-associated microbes are beneficial components of plant micro-ecosystems (Chebotar et al, 2015) because they provide protection against phytopathogens (Lindow and Brandl, 2003; Jetiyanon, 2007), enhance mineral nutrient acquisition (Elbeltagy et al, 2001; Johnson, 2008; Richardson et al, 2009), and help plants withstand abiotic stresses (Castiglioni et al, 2008; Zhang et al, 2008; Khan et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Endophytic Bacterium Pseudomonas fluorescens RG11 May Transform Tryptophan to Melatonin and Promote Endogenous Melatonin Levels in the Roots of Four Grape Cultivars

Jiao

Fan

et al. 2017

Front. Plant Sci.

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Endophytes have been verified to synthesize melatonin in vitro and promote abiotic stress-induced production of endogenous melatonin in grape (Vitis vinifera L.) roots. This study aimed to further characterize the biotransformation of tryptophan to melatonin in the endophytic bacterium Pseudomonas fluorescens RG11 and to investigate its capacity for enhancing endogenous melatonin levels in the roots of different grape cultivars. Using ultra performance liquid chromatography-tandem mass spectrometry combined with 15N double-labeled L-tryptophan as the precursor for melatonin, we detected isotope-labeled 5-hydroxytryptophan, serotonin, N-acetylserotonin, and melatonin, but tryptamine was not detected during the in vitro incubation of P. fluorescens RG11. Furthermore, the production capacity of these four compounds peaked during the exponential growth phase. RG11 colonization increased the endogenous levels of 5-hydroxytryptophan, N-acetylserotonin, and melatonin, but reduced those of tryptamine and serotonin, in the roots of the Red Globe grape cultivar under salt stress conditions. Quantitative real-time PCR revealed that RG11 reduced the transcription of grapevine tryptophan decarboxylase and serotonin N-acetyltransferase genes when compared to the un-inoculated control. These results correlated with decreased reactive oxygen species bursts and cell damage, which were alleviated by RG11 colonization under salt stress conditions. Additionally, RG11 promoted plant growth and enhanced the levels of endogenous melatonin in different grape cultivars. Intraspecific variation in the levels of melatonin precursors was found among four grape cultivars, and the associated root crude extracts appeared to significantly induce RG11 melatonin biosynthesis in vitro. Overall, this study provides useful information that enhances the existing knowledge of a potential melatonin synthesis pathway in rhizobacteria, and it reveals plant–rhizobacterium interactions that affect melatonin biosynthesis in plants subjected to abiotic stress conditions.

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“…However, this non-culture method is still not suitable for analyses of the plant endo-bacteriome because of the high sequence identity among bacterial 16S, plant Mt18S and Ct16S sequences. In a few previous studies, bacterial cells have been enriched from plant tissues by washing and vortexing [16,17] or the host DNA has been ltered out from the sequencing results [12,[18][19][20][21]. However, the former approach inevitably leads to an incomplete collection of endophytes, and the latter results in limited sequencing depth and low coverage of bacterial communities.…”

Section: Introductionmentioning

confidence: 99%

Quantitative and Qualitative Characterization of Plant Endo-bacteriome by Plant Dna-free Sequencing Method

Zhang¹,

Chen²,

Zhang³

et al. 2020

Preprint

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Background: Plant endophytic bacteria colonize plants’ internal tissues and interact with plants more closely than do epiphytic or environmental bacteria. However, the community structure of such endophytic bacteria could not be efficiently deciphered, and the microbiota abundance could not be quantified through absolute quantification. Application of 16S rRNA gene sequencing to characterize the plant endophytic community is greatly hindered by the high sequence identities among bacterial 16S rRNA, plant mitochondrial 18S rRNA and chloroplast 16S rRNA genes. This makes it difficult to identify bacterial sequences among total DNAs extracted from plant material.Results: We designed PCR primer sets that are able to specifically amplify bacterial DNAs, even when there are very few bacteria colonizing the plant material. We computationally and experimentally evaluated the specificity, coverage, and accuracy of the newly designed primer sets (322F/796R and 799F/1107R) and two widely used primer sets (338F/806R and 799F/1193R). When applied to a same planting-soil community through next generation sequencing (NGS), the four different primer sets revealed similar high-abundant taxa composition with variation in taxa abundance. Primer sets amplifying the same 16S variable regions generated more comparable sequencing results. When applied to a rice endo-bacteriome, both 799F/1107R and modified 322F-Dr/796Rs (Primer pair 322F/796R with a penultimate-base substitution in 322F) produced plant DNA-free bacterial amplicon libraries. Primer 322F-A/796R was then used through NGS to decipher the rice endo-bacteriomes. The rice root and leaf endo-bacteriomes shared 66.36% OTU identity but enriched different bacterial species. Within the same host genotype and soil type, the root endo-bacteriome was more stable than the leaf endo-bacteriome across individual plants. 322F-A/796R was used through absolute quantitative PCR to quantitate the population size of leaf or root endophytes, which revealed 106–107 and 109–1010 bacteria per gram fresh weight, respectively.Conclusions: This is the first study to develop plant DNA-free bacterial 16S amplification methods. The newly designed primer sets combined with NGS deciphered the rice endo-bacteriome structure, and absolute quantitative PCR quantitated the size of the endobacterial population. The protocols developed here are suitable for various plants, will significantly advance studies on plant endo-bacteriomes.

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Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice ( Oryza sativa L.)

Cited by 111 publications

References 39 publications

Phytomelatonin: Recent advances and future prospects

Phytomelatonin: Recent advances and future prospects

Endophytic Bacterium Pseudomonas fluorescens RG11 May Transform Tryptophan to Melatonin and Promote Endogenous Melatonin Levels in the Roots of Four Grape Cultivars

Quantitative and Qualitative Characterization of Plant Endo-bacteriome by Plant Dna-free Sequencing Method

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