Draft genomes and initial characterization of siderophore producing pseudomonads isolated from mine dump and mine drainage

Hofmann, Marika; Heine, Thomas; Schulz, Vivian; Hofmann, Sarah; Tischler, Dirk

doi:10.1016/j.btre.2019.e00403

Cited by 10 publications

(4 citation statements)

References 36 publications

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“…Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%) were the most abundantly annotated microbial genera in all samples (Fig 3). Although not consistent with our hypothesis, acid-tolerant bacteria from these genera have been isolated from other mines [17,[58][59][60][61][62][63][64], producing nutrients and mediating the flux of metal ions [65,66]. Species of Leptospirillum, Acidithiobacillus, Acidiphilium, and Thiobacillus were also present in the metagenome but at significantly lower abundance (<0.7%).…”

Section: Microbial Community Diversity and Compositioncontrasting

confidence: 70%

Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site

et al. 2020

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The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI "nt" database,~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal-(133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.

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Section: Microbial Community Diversity and Compositioncontrasting

confidence: 70%

Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site

et al. 2020

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“…Iron (Fe 3+ ) is an essential element for living organisms. It is involved in numerous cellular processes of various organisms [43]. The two siderophores: pyochelin (Pch) and pyoverdine (Pvd) observed within UY1PSABAL and UY1PSABAL2 help in iron assimilation.…”

Section: Hydrolytic Enzymes and Ion Uptake Systemmentioning

confidence: 99%

Whole-genome sequence of multi-drug resistant Pseudomonas aeruginosa strains UY1PSABAL and UY1PSABAL2 isolated from human broncho-alveolar lavage, Yaoundé, Cameroon

et al. 2020

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Pseudomonas aeruginosa has been implicated in a wide range of post-operation wound and lung infections. A wide range of acquired resistance and virulence markers indicate surviving strategy of P. aeruginosa. Complete-genome analysis has been identified as efficient approach towards understanding the pathogenicity of this organism. This study was designed to sequence the entire genome of P. aeruginosa UY1PSABAL and UY1PSABAL2; determine drug-resistance profiles and virulence factors of the isolates; assess factors that contribute toward stability of the genomes; and thereafter determine evolutionary relationships between the strains and other isolates from similar sources. The genomes of the MDR P. aeruginosa UY1PSABAL and UY1PSABAL2 were sequenced on the Illumina Miseq platform. The raw sequenced reads were assessed for quality using FastQC v.0.11.5 and filtered for low quality reads and adapter regions using Trimmomatic v.0.36. The de novo genome assembly was made with SPAdes v.3.13 and annotated using Prokka v.2.1.1 annotation pipeline; Rapid Annotation using Subsytems Technology (RAST) server v.2.0; and PATRIC annotation tool v.3.6.2. Antimicrobial resistance genes and virulence determinants were searched through the functional annotation data generated from Prokka, RAST and PATRIC annotation pipelines; In addition to ResFinder and Comprehensive Antibiotic Resistance Database (CARD) which were employed to determine resistance genes. The PHAge Search Tool Enhanced Release (PHASTER) web server was used for the rapid identification and annotation of prophage sequences within bacterial genome. Predictive secondary metabolites were identified with AntiSMASH v.5.0. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and cas genes regions were also investigated with the CRISPRone and CRISPRFinder server. The genome sizes of 7.0 and 6.4 Mb were

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“…The genomic DNA of N. simplex 3E and the type strain P. chlororaphis DSM 50083 were isolated using an adapted phenol-chloroform method as described previously [ 31 ]. The preparation of the library, genome sequencing, assembly annotation, and analysis were done as described elsewhere [ 31 , 33 ].…”

Section: Methodsmentioning

confidence: 99%

Screening for Microbial Metal-Chelating Siderophores for the Removal of Metal Ions from Solutions

et al. 2021

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To guarantee the supply of critical elements in the future, the development of new technologies is essential. Siderophores have high potential in the recovery and recycling of valuable metals due to their metal-chelating properties. Using the Chrome azurol S assay, 75 bacterial strains were screened to obtain a high-yield siderophore with the ability to complex valuable critical metal ions. The siderophore production of the four selected strains Nocardioides simplex 3E, Pseudomonas chlororaphis DSM 50083, Variovorax paradoxus EPS, and Rhodococcus erythropolis B7g was optimized, resulting in significantly increased siderophore production of N. simplex and R. erythropolis. Produced siderophore amounts and velocities were highly dependent on the carbon source. The genomes of N. simplex and P. chlororaphis were sequenced. Bioinformatical analyses revealed the occurrence of an achromobactin and a pyoverdine gene cluster in P. chlororaphis, a heterobactin and a requichelin gene cluster in R. erythropolis, and a desferrioxamine gene cluster in N. simplex. Finally, the results of the previous metal-binding screening were validated by a proof-of-concept development for the recovery of metal ions from aqueous solutions utilizing C18 columns functionalized with siderophores. We demonstrated the recovery of the critical metal ions V(III), Ga(III), and In(III) from mixed metal solutions with immobilized siderophores of N. simplex and R. erythropolis.

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Draft genomes and initial characterization of siderophore producing pseudomonads isolated from mine dump and mine drainage

Abstract: HighlightsHigh and stable siderophore production.Identification of siderophore biosynthesis gene clusters.Beech wood hydrolysate as alternative carbon source.

Cited by 10 publications

References 36 publications

Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site

Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site

Whole-genome sequence of multi-drug resistant Pseudomonas aeruginosa strains UY1PSABAL and UY1PSABAL2 isolated from human broncho-alveolar lavage, Yaoundé, Cameroon

Screening for Microbial Metal-Chelating Siderophores for the Removal of Metal Ions from Solutions

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