Characteristics and diversity of endophytic bacteria in Panax notoginseng under high temperature analysed using full-length 16S rRNA sequencing

Liang, Zhenting; Lin, Xianjing; Liao, Yiqun; Tang, Ting

doi:10.1007/s00203-022-03043-0

Cited by 5 publications

(5 citation statements)

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“…We identified the 16S rRNA genes from the accurate HiFi long reads by INFERNAL ( Nawrocki and Eddy, 2013 ), and found a total number of 54,135 16S rRNA genes. Unlike the previous study using the PCR amplification and PacBio HiFi sequencing to acquire the full-length 16S rRNA gene sequences ( Liang et al, 2022 ), the present study directly identified the full-length 16S rRNA gene sequences from the PacBio HiFi long reads, without any PCR amplification. Of the identified 16S rRNA genes, most of them (67%) ranged from 1,500 to 1,520 bp, with the length peaked at 1,512 bp ( Figure 6A ), consistent with the reported length of microbial full-length 16S rRNA genes.…”

Section: Resultsmentioning

confidence: 99%

“…Besides, high proportion of novel genomes were generated, which recovered 89 novel genomes (26% of the total assembled genomes) from the chicken gut microbiomes by using 332 Gb of HiFi reads ( Zhang Y. et al, 2022 ). In addition, HiFi long reads also enabled the analysis of full-length 16S rRNA genes covering all hypervariable regions, which could provide more accurate taxonomic classification for microorganisms ( Liang et al, 2022 ). In this study, we used the HiFi long reads to construct the microbial genomes for microorganisms in AD of food waste, and analyzed the full-length 16S rRNA genes identified from the sequenced long reads to investigate the microbial communities.…”

Section: Introductionmentioning

confidence: 99%

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Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing

Jiang

Wang

et al. 2023

Front. Microbiol.

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BackgroundAnaerobic digestion (AD) is important in treating of food waste, and thousands of metagenome-assembled genomes (MAGs) have been constructed for the microbiome in AD. However, due to the limitations of the short-read sequencing and assembly technologies, most of these MAGs are grouped from hundreds of short contigs by binning algorithms, and the errors are easily introduced.ResultsIn this study, we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥18 types of standard tRNA genes, and 39 are circular complete genomes. In comparison with the published short-read derived MAGs for AD, we found 23 genomes with average nucleotide identity less than 95% to any known MAGs. Besides, our HiFi-derived genomes have much higher average contig N50 size, slightly higher average genome size and lower contamination. GTDB-Tk classification of these genomes revealed two genomes belonging to novel genus and four genomes belonging to novel species, since their 16S rRNA genes have identities lower than 95 and 97% to any known 16S rRNA genes, respectively. Microbial community analysis based on the these assembled genomes reveals the most predominant phylum was Thermotogae (70.5%), followed by Euryarchaeota (6.1%), and Bacteroidetes (4.7%), and the most predominant bacterial and archaeal genera were Defluviitoga (69.1%) and Methanothrix (5.4%), respectively. Analysis of the full-length 16S rRNA genes identified from the HiFi reads gave similar microbial compositions to that derived from the 60 assembled genomes.ConclusionHigh-fidelity sequencing not only generated microbial genomes with obviously improved quality but also recovered a substantial portion of novel genomes missed in previous short-read based studies, and the novel genomes will deepen our understanding of the microbial composition in AD of food waste.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing

Jiang

Wang

et al. 2023

Front. Microbiol.

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“…Streptococcus has been established as an endophyte in crops, such as maize ( 141 ). The similarity of metabolic pathways such as carbohydrate and amino acid metabolism, metabolism of terpenoids and polyketide between endophytic bacteria and different plants Cinnamomum camphora ( 142 ), and P. notoginseng ( 143 ) have been reported, suggesting a close symbiotic association with the host plant. Secondary metabolites regulate plant growth, photosynthesis, signal transduction, along with development and can be enhanced by endophytic bacteria ( 144 ).…”

Section: Discussionmentioning

confidence: 99%

Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa , a Himalayan medicinal herb

Tamang,

Swarnkar,

Kumar

et al. 2023

Microbiol Spectr

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Picrorhiza kurrooa an endangered high-altitude Himalayan medicinal herb, is used as a potent hepatoprotective due to the presence of various secondary metabolites, with picrosides being the most bioactive. In-vitro propagation is used as a sustainable strategy for its conservation and cultivation. The in-vitro propagation produces P. kurrooa plants (Tc) in mass, but these plants have reduced secondary metabolites (especially picrosides) compared to plants growing in their natural habitats (Wt). Therefore, considering the well-established role of microbes in secondary metabolite biosynthesis, in this study, endomicrobiome of P. kurroa plants (Tc and Wt) was explored. Using high-throughput DNA-sequencing, the endophytic communities associated with leaves, roots, and rhizomes of Wt and Tc plants were characterized. Diversity analysis revealed a loss of diversity during in-vitro propagation, and the abundant phyla were Proteobacteria, Bacteroidetes, Parcubacteria (OD1), Firmicutes, and Verrucomicrobia. Besides, the presence of distinct genera specific to different parts of Wt plants was also revealed. Quantification of secondary metabolites demonstrated the reduced accumulation of picrosides and intermediates of picroside biosynthesis in the Tc plants compared to Wt plants. Host-secondary metabolite production was positively correlated to microbial community abundance, suggesting a dynamic interplay of host-endomicrobiota interaction. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite biosynthesis (especially MVA/MEP and phenylpropanoid/shikimate pathway involved in picrosides biosynthesis) in the associated-endophytic community with predominance in roots and rhizomes of Wt plants. This investigation provides novel insight into the change in the endomicrobiome of Wt and Tc plants and their correlation to the biosynthesis of secondary metabolites, and that needs to be considered for cultivation practices. IMPORTANCE Picrorhiza kurrooa is a major source of picrosides, potent hepatoprotective molecules. Due to the ever-increasing demands, overexploitation has caused an extensive decline in its population in the wild and placed it in the endangered plants' category. At present plant in-vitro systems are widely used for the sustainable generation of P. kurrooa plants, and also for the conservation of other commercially important, rare, endangered, and threatened plant species. Furthermore, the in-vitro -generated plants had reduced content of therapeutic secondary metabolites compared to their wild counterparts, and the reason behind, not well-explored. Here, we revealed the loss of plant-associated endophytic communities during in-vitro propagation of P. kurrooa plants which also correlated to in-planta secondary metabolite biosynthesis. Therefore, this study emphasized to consider the essential role of plant-associated endophytic communities in in-vitro practices which may be the possible reason for reduced secondary metabolites in in-vitro plants.

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“…The overall compositions of microbial communities were viewed across seasons and treatments at the order level [69]. Potentially pathogenic microbes (PPM) were identified as ESVs with a 100% match [70] to one or more known or suspected pathogens for humans, animals, vascular plants, and/or macroalgae based on a literature review [9,[33][34][35][36][37][38][39][40] (Table S1). PPM proportions were square root transformed to reduce the influence of dominant taxa [149], and differences in community composition were identified using a two-way crossed analysis of similarities (ANOSIM) [150] and visualized via non-metric multidimensional scaling (nMDS) plots based on Bray-Curtis similarities [151].…”

Section: Bioinformatics and Statistical Analysesmentioning

confidence: 99%

“…Some particles are rejected prior to digestion in the form of pseudofeces, while others are ingested and either assimilated into biomass or excreted as feces [30][31][32]. Any or all of these particle fractions may contain bacteria that are pathogenic to a wide variety of species inhabiting coastal systems, including humans [2,5,8], animals [33][34][35], vascular plants [36,37], and macroalgae [38][39][40]. Pathogens that are ingested and remain in oyster guts and tissues present a direct health risk to oyster consumers.…”

Section: Introductionmentioning

confidence: 99%

Oyster Reefs Are Reservoirs for Potential Pathogens in a Highly Disturbed Subtropical Estuary

Sweat,

Busch,

Craig

et al. 2023

Environments

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Estuaries worldwide are grappling with deteriorating water quality and benthic conditions that coincide with the rising detection of pathogenic and potentially pathogenic microbes (PPM). Both indigenous PPM and those that enter estuaries through urban and agricultural runoff are funneled through suspension-feeding organisms and deposited onto the benthos, where they can be moved through food webs. This study explored PPM communities in the Indian River Lagoon system, a biodiverse but urbanized estuary in east central Florida (USA). PPM were surveyed in estuary water, at stormwater outfalls, and in biodeposits of a key suspension feeder, the eastern oyster Crassostrea virginica. A total of 52 microbial exact sequence variants, with per-sample relative abundances up to 61.4%, were identified as PPM. The biodeposits contained relatively more abundant and diverse PPM than the water samples. PPM community composition also differed between seasons and between biodeposits and water. The community differences were driven primarily by Vibrio and Pseudoalteromonas spp. This investigation provides evidence that, through biodeposition, oyster reefs in the IRL estuary are a reservoir for PPM, and it documents some taxa of concern that should be conclusively identified and investigated for their pathogenicity and potential to pervade food webs and fisheries.

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Characteristics and diversity of endophytic bacteria in Panax notoginseng under high temperature analysed using full-length 16S rRNA sequencing

Cited by 5 publications

References 65 publications

Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing

Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing

Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa , a Himalayan medicinal herb

Oyster Reefs Are Reservoirs for Potential Pathogens in a Highly Disturbed Subtropical Estuary

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