Analysis of the Endophytic Bacteria Community Structure and Function of Panax notoginseng Based on High-Throughput Sequencing

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

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The Relationship between the Community Structure and Function of Bacterioplankton and the Environmental Response in Qingcaosha Reservoir

Water ◽

10.3390/w13223155 ◽

2021 ◽

Vol 13 (22) ◽

pp. 3155

Author(s):

Shumin Liu ◽

Fengbin Zhao ◽

Xin Fang

Keyword(s):

Water Quality ◽

Community Structure ◽

High Throughput Sequencing ◽

Scientific Basis ◽

Vital Role ◽

Structure And Function ◽

Environmental Response ◽

Temporal And Spatial ◽

Density And Biomass ◽

And Function

Phytoplankton and bacterioplankton play a vital role in the structure and function of aquatic ecosystems, and their activity is closely linked to water eutrophication. However, few researchers have considered the temporal and spatial succession of phytoplankton and bacterioplankton, and their responses to environmental factors. The temporal and spatial succession of bacterioplankton and their ecological interaction with phytoplankton and water quality were analyzed using 16S rDNA high-throughput sequencing for their identification, and the functions of bacterioplankton were predicted. The results showed that the dominant classes of bacterioplankton in the Qingcaosha Reservoir were Gammaproteobacteria, Alphaproteobacteria, Actinomycetes, Acidimicrobiia, and Cyanobacteria. In addition, the Shannon diversity indexes were compared, and the results showed significant temporal differences based on monthly averaged value, although no significant spatial difference. The community structure was found to be mainly influenced by phytoplankton density and biomass, dissolved oxygen, and electrical conductivity. The presence of Pseudomonas and Legionella was positively correlated with that of Pseudanabaena sp., and Sphingomonas and Paragonimus with Melosira granulata. On the contrary, the presence of Planctomycetes was negatively correlated with Melosira granulata, as was Deinococcus-Thermus with Cyclotella sp. The relative abundance of denitrifying bacteria decreased from April to December, while the abundance of nitrogen-fixing bacteria increased. This study provides a scientific basis for understanding the ecological interactions between bacteria, algae, and water quality in reservoir ecosystems.

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Community structure and function of cultivable Endophytic Bacteria isolated from four Moss species in Qilian Mountain

Symbiosis ◽

10.1007/s13199-020-00669-w ◽

2020 ◽

Vol 80 (3) ◽

pp. 257-267

Author(s):

Xiaojun Lan ◽

Heng Zhou ◽

Tuo Yao ◽

Wanqing Dong ◽

Jiangui Zhang ◽

...

Keyword(s):

Community Structure ◽

Endophytic Bacteria ◽

Structure And Function ◽

Qilian Mountain ◽

Moss Species ◽

And Function

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Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology

International Journal of Molecular Sciences ◽

10.3390/ijms21228774 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8774

Author(s):

Natalia Komarova ◽

Daria Barkova ◽

Alexander Kuznetsov

Keyword(s):

Nucleic Acid ◽

High Throughput ◽

High Throughput Sequencing ◽

Combinatorial Libraries ◽

Structure And Function ◽

Huge Number ◽

Systematic Evolution ◽

And Function ◽

Exponential Enrichment

Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.

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Applications of high-throughput sequencing to chromatin structure and function in mammals

F1000 Biology Reports ◽

10.3410/b1-32 ◽

2009 ◽

Vol 1 ◽

Author(s):

Ian Dunham

Keyword(s):

High Throughput ◽

Chromatin Structure ◽

High Throughput Sequencing ◽

Structure And Function ◽

And Function

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The citrus microbiome: from structure and function to microbiome engineering and beyond

Phytobiomes Journal ◽

10.1094/pbiomes-11-20-0084-rvw ◽

2021 ◽

Author(s):

Yunzheng Zhang ◽

Pankaj Trivedi ◽

jin xu ◽

M. Caroline Roper ◽

Nian Wang

Keyword(s):

Artificial Intelligence ◽

High Throughput ◽

High Throughput Sequencing ◽

Plant Root ◽

Rapid Development ◽

Structure And Function ◽

Omics Technologies ◽

Microbiome Research ◽

Citrus Root ◽

And Function

Individual microbes often have defined relationship with their hosts that include beneficial, commensal, and pathogenic interactions. However, at the community level, plant microbiomes are considered to play a beneficial role in protecting the plant from potential pathogens, acquiring nutrients, and improving growth and production. Citrus is a globally important perennial fruit crop and its production faces many challenges. There have been tremendous interests to explore the structure and function of citrus microbiome and engineer citrus microbiome to address various challenges. In this review, we summarized recent advances in understanding of citrus microbiome, including the composition and function of microbiome in the rhizosphere, rhizoplane, endorhiza, core members and their functional traits. We conducted comparisons of citrus root-associated microbiome with other plant root-associated microbiomes. We also present a perspective on how incoming pathogens interact with the resident microbial community and their outcomes. Despite the promising potential of the citrus microbiome to combat disease, harnessing the citrus microbiome for beneficial applications remains in its infancy. We envision that rapid development of high throughput sequencing and multi-omics technologies, artificial intelligence, consortia of microbes, genome editing technology, and high-throughput culturing present many exciting opportunities to citrus microbiome research and microbial engineering to improve citrus health and productivity.

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Community Structure and Function of Epiphytic Bacteria Associated With Myriophyllum spicatum in Baiyangdian Lake, China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.705509 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lei Sun ◽

Jiashuo Wang ◽

Yangyang Wu ◽

Tianyu Gao ◽

Cunqi Liu

Keyword(s):

Community Structure ◽

Bacterial Community ◽

High Throughput ◽

High Throughput Sequencing ◽

Myriophyllum Spicatum ◽

Epiphytic Bacteria ◽

Baiyangdian Lake ◽

Operational Taxonomic Units ◽

The Common ◽

And Function

Epiphytic bacteria on the surfaces of submerged macrophytes play important roles in the growth of the host plant, nutrient cycling, and the conversion of pollutants in aquatic systems. A knowledge of the epiphytic bacterial community structure could help us to understand these roles. In this study, the abundance, diversity, and functions of the epiphytic bacterial community of Myriophyllum spicatum collected from Baiyangdian Lake in June, August, and October 2019 were studied using quantitative PCR (qPCR), high-throughput sequencing, and the prediction of functions. An analysis using qPCR showed that the epiphytic bacteria were the most abundant in October and the least abundant in August. High-throughput sequencing revealed that Proteobacteria, Gammaproteobacteria, and Aeromonas were the dominant phylum, class, and genus in all the samples. The common analyses of operational taxonomic units (OTUs), NMDS, and LDA showed that the epiphytic bacterial communities were clustered together based on the seasons. The results of a canonical correlation analysis (CCA) showed that the key water quality index that affected the changes of epiphytic bacterial community of M. spicatum was the total phosphorus (TP). The changes in abundance of Gammaproteobacteria negatively correlated with the TP. Predictive results from FAPROTAX showed that the predominant biogeochemical cycle functions of the epiphytic bacterial community were chemoheterotrophy, nitrate reduction, and fermentation. These results suggest that the epiphytic bacterial community of M. spicatum from Baiyangdian Lake varies substantially with the seasons and environmental conditions.

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