Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil

Rodrigues, Edmo Montes; Vidigal, Pedro Marcus Pereira; Pylro, Victor Satler; Morais, Daniel; Leite, Laura Hora Rios; Roesch, Luiz Fernando Würdig; Tótola, Marcos Rogério

doi:10.1016/j.bjm.2016.09.014

Cited by 9 publications

(6 citation statements)

References 7 publications

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“…Thus, these degradation functions may be involved in disease resistance of P. notoginseng . Moreover, previous studies reported that many microbes can degrade plant exudates and stable pollutants in soil, such as polycyclic aromatic hydrocarbon, benzoate and chlorophenols (Orro et al, 2015; Park & Kim, 2003; Rodrigues et al, 2016; Solvanikova & Golovleva, 2015). The prevalence of these degradation pathways may also suggest that P. notoginseng core rhizosphere microbes degrade notoginseng allelochemicals, such as phenols (Bi et al, 2010) and saponins (Yang et al, 2015), as well as potential exogenous pollutants to reduce the autotoxicity of P. notoginseng .…”

Section: Discussionmentioning

confidence: 99%

Core rhizosphere microbiome ofPanax notoginsengand its associations with belowground biomass and saponin contents

Wei

Zhang

et al. 2022

Environmental Microbiology

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The core rhizosphere microbiome is critical for plant fitness. However, its contribution to the belowground biomass and saponin contents of Panax notoginseng remains unclear. High‐throughput sequencing of amplicon and metagenome was performed to obtain the microbiome profiles and functional traits in P. notoginseng rhizosphere across a large spatial scale. We obtained 639 bacterial and 310 fungal core OTUs, which were mainly affected by soil pH and organic matter (OM). The core taxa were grouped into four ecological clusters (i.e. high pH, low pH, high OM and low OM) for sharing similar habitat preferences. Furthermore, structural equation modelling (SEM) and correlation analyses revealed that the diversity and composition of core microbiomes, as well as the metagenome‐derived microbial functions, were related to belowground biomass and saponin contents. Key microbial genera related to the two plant indicators were also identified. In short, this study explored the main driving environmental factors of core microbiomes in the P. notoginseng rhizosphere and revealed that the core microbiomes and microbial functions potentially contributed to the belowground biomass and saponin contents of the plant. This work may enhance our understanding of interactions between microbes and perennial plants and improve our ability to manage root microbiota for the sustainable production of herbal medicine.

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Section: Discussionmentioning

confidence: 99%

Core rhizosphere microbiome ofPanax notoginsengand its associations with belowground biomass and saponin contents

Wei

Zhang

et al. 2022

Environmental Microbiology

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“…[ 8 , 9 ], a result of the physiological and biochemical pressures imposed by the environmental conditions under which they live [ 10 ]. Their activity in the degradation of polycyclic aromatic hydrocarbon [ 11 , 12 ] focused on them as potential xenobiotic bioremediators.…”

Section: Introductionmentioning

confidence: 99%

Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans

et al. 2020

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Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p ≤ 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).

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“…Different studies revealed that some Nocardia spp. harbor lcp genes, which are responsible for the initiation of the biodegradation of polymeric materials such as rubber ( 4 , 7 – 10 ). The isolated strain BSTN01 was obtained from the stored water in latex-collecting cups (used to collect the freshly tapped latex from the Hevea brasiliensis trees) thrown away near a local rubber processing unit in Tripura, India.…”

Section: Announcementmentioning

confidence: 99%

Whole-Genome Shotgun (WGS) Sequence of cis -Isoprene Polymer-Degrading Nocardia sp. strain BSTN01

Sarkar

Mandal

Ghati³

et al. 2022

Microbiol Resour Announc

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Species belonging to the genus Nocardia are known to be facultative human pathogens. There are also reports of Nocardia species capable of degrading various forms of rubber. Here, we report the whole-genome shotgun (WGS) sequence of Nocardia sp. strain BSTN01, isolated from stored water in latex-collecting cups thrown away near a local rubber processing unit in Tripura, India.

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Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil

Abstract: Here, we report the draft genome sequence and annotation of Nocardia farcinica TRH1, a petroleum hydrocarbons degrading Actinobacteria isolated from the coastal water of Trindade Island, Brazil.

Cited by 9 publications

References 7 publications

Core rhizosphere microbiome ofPanax notoginsengand its associations with belowground biomass and saponin contents

Core rhizosphere microbiome ofPanax notoginsengand its associations with belowground biomass and saponin contents

Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil; A Comparison with Species Isolated from Humans

Whole-Genome Shotgun (WGS) Sequence of cis -Isoprene Polymer-Degrading Nocardia sp. strain BSTN01

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