The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing

Abstract

In the present study, the shotgun high throughput metagenomic sequencing was implemented to globally capture the features of Taxus rhizosphere microbiome. Total reads could be assigned to 6925 species belonging to 113 bacteria phyla and 301 species of nine fungi phyla. For archaea and virus, 263 and 134 species were for the first time identified, respectively. More than 720,000 Unigenes were identified by clean reads assembly. The top five assigned phyla were Actinobacteria (363,941 Unigenes), Proteobacteria (182,053), Acidobacteria (44,527), Ascomycota (fungi; 18,267), and Chloroflexi (15,539). KEGG analysis predicted numerous functional genes; 7101 Unigenes belong to "Xenobiotics biodegradation and metabolism." A total of 12,040 Unigenes involved in defense mechanisms (e.g., xenobiotic metabolism) were annotated by eggNOG. Talaromyces addition could influence not only the diversity and structure of microbial communities of Taxus rhizosphere, but also the relative abundance of functional genes, including metabolic genes, antibiotic resistant genes, and genes involved in pathogen-host interaction, bacterial virulence, and bacterial secretion system. The structure and function of rhizosphere microbiome could be sensitive to non-native microbe addition, which could impact on the pollutant degradation. This study, complementary to the amplicon sequencing, more objectively reflects the native microbiome of Taxus rhizosphere and its response to environmental pressure, and lays a foundation for potential combination of phytoremediation and bioaugmentation.

Implementation of Omics Research to Enhance Phytoremediation Efficiency - a Review

“…The same study showed, that genes involved in the transformation and degradation of organic pollutants are also mostly present in plasmids [24]. Such knowledge has already been applied, and plasmids with genes responsible for toluene degradation were successfully transferred to aerial plant endophytes and increased the total degradation of contaminant that would have been volatilized [26]. Besides, metagenomic research performed in changing environmental conditions showed that the microbial communities in terms of its genetic and taxonomic composition could be linked to its activity to metabolize carbon.…”

“…For example, experiment from 2012 showed, that exudate produced by wild rye exposed to hydrocarbons were not as repressive as exudate from wild rye grown on an uncontaminated medium, which overall demonstrated that plants might alter the extent to which they will promote total rhizosphere biodegradation [25]. Thus, it has to be taken into consideration that the overall degree to which plants can exert control over bacterial and fungi communities strictly depends on the concentration of given contaminant and its overall severity of toxic effects [26].…”

“…In the study by Hao et al shotgun high throughput metagenomic sequencing was used in order to capture the PAHs degrading features of Taxus rhizosphere microbiome. Study showed numerous functional genes associated with biodegradation and metabolism of xenobiotics as well as multiple genes involved in a range of defence mechanisms against organic pollutants [26].…”

“…Analysis of an wastewater treatment plants microbial communities and their potential to metabolize pharmaceuticals pharmaceuticals 2016 [24] Understanding the mechanism and function of plant growth-promoting rhizobacteria (PGPR) none 2017 [12] Analysis of the response of microbial metagenome to polycyclic aromatic hydrocarbons (PAHs) degradation in the rice rhizosphere PAHs 2015 [22] Perspectives of lindane (γ-hexachlorocyclohexane) biodegradation lindane 2018 [23] Identification of the potential for toluene biodegradation in the vadose zone of a poplar toluene 2019 [21] Analysis of the influence of cadmium contamination on bioenergy cropping and microbial composition of cadmium contaminated soil cadmium 2017 [6] Analysis of the potential of Taxus rhizosphere microbiome for bioremediation and phytoremediation none 2018 [26] Analysis of rhizosphere microorganisms of PAHs contaminated soil planted with barley and alfalfa PAHs 2018 [23] Identification of the influence of microbial community on the efficiency of metal phytoremediation by Sedum plumbizincicola cadmium and zinc 2017 [27] 3. Plants genomic and transcriptomic studies in the aspects of environmental contamination…”

The Utility of Electrochemical Systems in Microbial Degradation of Polycyclic Aromatic Hydrocarbons: Discourse, Diversity and Design

“…However, the PCR bias cannot be avoided and the information about microbial function is not provided. The shotgun metagenomic sequencing (Hao et al, 2018b), complementary to the amplicon sequencing, could more objectively reflect the microbiome status quo and dynamics of anode biofilm, and should be utilized in the future study.…”