Phenotypic and genomic characterization of the antimicrobial producer Rheinheimera sp. EpRS3 isolated from the medicinal plant Echinacea purpurea: insights into its biotechnological relevance

Presta, Luana; Bosi, Emanuele; Fondi, Marco; Maida, Isabel; Perrin, Elena; Miceli, Elisangela; Maggini, Valentina; Bogani, Patrizia; Firenzuoli, Fabio; Pilato, Vincenzo Di; Rossolini, Gian María; Mengoni, Alessio; Fani, Renato

doi:10.1016/j.resmic.2016.11.001

Cited by 31 publications

(23 citation statements)

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“…EpRS3 TolC in the mechanisms leading to the interaction with the protozoan cell, as previously documented in Legionella pneumophila toward Paramecium tetraurelia (Nishida et al, 2018). Indeed, it has been previously demonstrated that EpRS3 genome harbors several genes encoding for components of efflux pump systems, like AcrB, belonging to the AcrAB/TolC system, or MdtB and MdtC, these last forming a heteromultimer complex, a subunit of MdtABC-TolC efflux pump (Presta et al, 2017). This information will help in elucidating the molecular mechanisms leading to the eukaryotic cell structures damage, to protist death, and to the possible re-entry of Rheinheimera sp.…”

Section: Discussionmentioning

confidence: 99%

“…Rheinheimera EpRS3 shows resistance to several antibiotic compounds (Mengoni et al, 2014) and can inhibit the growth of various bacteria isolated from both E. purpurea rhizospheric soil and plant tissues (Maida et al, 2016). Additionally, EpRS3 can inhibit the growth of opportunistic human pathogenic bacteria belonging to the Burkholderia cepacia complex (Bcc) (Chiellini et al, 2017), as well as the growth of different bacterial pathogens (e.g., Acinetobacter baumanni , Klebsiella pneumoniae ) the majority of which exhibit a multi-drug-resistance phenotype (Presta et al, 2017). It has been hypothesized that the production of antimicrobial compounds, and the subsequent antagonistic activity of some bacterial strains belonging to the same or different taxa, might play a (key) role in driving the structuring of microbial communities interacting with eukaryotic macro-organisms (Maida et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Harmful Effect of Rheinheimera sp. EpRS3 (Gammaproteobacteria) Against the Protist Euplotes aediculatus (Ciliophora, Spirotrichea): Insights Into the Ecological Role of Antimicrobial Compounds From Environmental Bacterial Strains

et al. 2019

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Rheinheimera sp. strain EpRS3, isolated from the rhizosphere of Echinacea purpurea , is already known for its ability to produce antibacterial compounds. By use of culture experiments, we verified and demonstrated its harmful effect against the ciliated protist Euplotes aediculatus (strain EASCc1), which by FISH experiments resulted to harbor in its cytoplasm the obligate bacterial endosymbiont Polynucleobacter necessarius ( Betaproteobacteria ) and the secondary endosymbiont “ Candidatus Nebulobacter yamunensis” ( Gammaproteobacteria ). In culture experiments, the number of ciliates treated both with liquid broth bacteria-free (Supernatant treatment) and bacteria plus medium (Tq treatment), decreases with respect to control cells, with complete disappearance of ciliates within 6 h after Tq treatment. Results suggest that Rheinheimera sp. EpRS3 produces and releases in liquid culture one or more bioactive molecules affecting E. aediculatus survival. TEM analysis of control (not treated) ciliates allowed to morphologically characterize both kind of E. aediculatus endosymbionts. In treated ciliates, collected soon after the arising of cell suffering leading to death, TEM observations revealed some ultrastructural damages, indicating that P. necessarius endosymbionts went into degradation and vacuolization after both Supernatant and Tq treatments. Additionally, TEM investigation showed that when the ciliate culture was inoculated with Tq treatment, both a notable decrease of P. necessarius number and an increase of damaged and degraded mitochondria occur. FISH experiments performed on treated ciliates confirmed TEM results and, by means of the specific probe herein designed, disclosed the presence of Rheinheimera sp. EpRS3 both inside phagosomes and free in cytoplasm in ciliates after Tq treatment. This finding suggests a putative ability of Rheinheimera sp. EpRS3 to reintroduce itself in the environment avoiding ciliate digestion.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Harmful Effect of Rheinheimera sp. EpRS3 (Gammaproteobacteria) Against the Protist Euplotes aediculatus (Ciliophora, Spirotrichea): Insights Into the Ecological Role of Antimicrobial Compounds From Environmental Bacterial Strains

et al. 2019

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“…16S rRNA gene sequences from strains belonging to K. oxytoca were selected from NCBI ftp site to run a phylogenetic analysis. Sequence alignment and phylogenetic tree were obtained as previously described in Presta et al (2017) [ 30 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

et al. 2018

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BackgroundKlebsiella oxytoca DSM 29614 - isolated from acid mine drainages - grows anaerobically using Fe(III)-citrate as sole carbon and energy source, unlike other enterobacteria and K. oxytoca clinical isolates. The DSM 29614 strain is multi metal resistant and produces metal nanoparticles that are embedded in its very peculiar capsular exopolysaccharide. These metal nanoparticles were effective as antimicrobial and anticancer compounds, chemical catalysts and nano-fertilizers.ResultsThe DSM 29614 strain genome was sequenced and analysed by a combination of in silico procedures. Comparative genomics, performed between 85 K. oxytoca representatives and K. oxytoca DSM 29614, revealed that this bacterial group has an open pangenome, characterized by a very small core genome (1009 genes, about 2%), a high fraction of unique (43,808 genes, about 87%) and accessory genes (5559 genes, about 11%). Proteins belonging to COG categories “Carbohydrate transport and metabolism” (G), “Amino acid transport and metabolism” (E), “Coenzyme transport and metabolism” (H), “Inorganic ion transport and metabolism” (P), and “membrane biogenesis-related proteins” (M) are particularly abundant in the predicted proteome of DSM 29614 strain. The results of a protein functional enrichment analysis - based on a previous proteomic analysis – revealed metabolic optimization during Fe(III)-citrate anaerobic utilization. In this growth condition, the observed high levels of Fe(II) may be due to different flavin metal reductases and siderophores as inferred form genome analysis. The presence of genes responsible for the synthesis of exopolysaccharide and for the tolerance to heavy metals was highlighted too. The inferred genomic insights were confirmed by a set of phenotypic tests showing specific metabolic capability in terms of i) Fe2+ and exopolysaccharide production and ii) phosphatase activity involved in precipitation of metal ion-phosphate salts.ConclusionThe K. oxytoca DSM 29614 unique capabilities of using Fe(III)-citrate as sole carbon and energy source in anaerobiosis and tolerating diverse metals coincides with the presence at the genomic level of specific genes that can support i) energy metabolism optimization, ii) cell protection by the biosynthesis of a peculiar exopolysaccharide armour entrapping metal ions and iii) general and metal-specific detoxifying activities by different proteins and metabolites.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1330-5) contains supplementary material, which is available to authorized users.

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“…BLAST results demonstrated that both genes are homologous to their counterparts in Rheinheimera (Blastp, identity 72% for ohr (WP_127019447.1) and 70% for ohrR (WP_127022368.1)). Rheinheimera is frequently isolated from plant-associated materials including rhizosphere soil and roots [59,60], indicating that the ohr and ohrR genes of Bin79 might have been acquired from other soil-borne microbes, such as Rheinheimera, via HGT, which endowed Bin79 with resistance to plant OHPs. The results of Alien_Hunter analysis further demonstrated that the ohr and ohrR genes were located within a genomic region that was acquired via HGT.…”

Section: Figurementioning

confidence: 99%

Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics

Zhang

Wang

et al. 2020

Microorganisms

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Maintaining integrity of the plant cell walls is critical for plant health, however, our previous study showed that Cellvibrio, which is recognized by its robust ability to degrade plant cell walls, was enriched from the citrus rhizosphere to the rhizoplane (i.e., the root surface). Here we investigated the mechanisms underlying the rhizosphere-to-rhizoplane enrichment of Cellvibrio through genome-centric metagenomics and metatranscriptomics analyses. We recovered a near-complete metagenome-assembled genome representing a potentially novel species of Cellvibrio, herein designated Bin79, with genome size of 5.71 Mb across 11 scaffolds. Differential gene expression analysis demonstrated that plant cell wall degradation genes were repressed, whereas genes encoding chitin-degrading enzymes were induced in the rhizoplane compared with the rhizosphere. Enhanced expression of multi-drug efflux genes and iron acquisition- and storage-associated genes in the rhizoplane indicated mechanisms by which Bin79 competes with other microbes. In addition, genes involved in repelling plant immune responses were significantly activated in the rhizoplane. Comparative genomics analyses with five related Cellvibrio strains showed the importance of gene gain events for the rhizoplane adaptation of Bin79. Overall, this study characterizes a novel Cellvibrio strain and indicates the mechanisms involved in its adaptation to the rhizoplane from meta-omics data without cultivation.

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Phenotypic and genomic characterization of the antimicrobial producer Rheinheimera sp. EpRS3 isolated from the medicinal plant Echinacea purpurea: insights into its biotechnological relevance

Cited by 31 publications

References 32 publications

Harmful Effect of Rheinheimera sp. EpRS3 (Gammaproteobacteria) Against the Protist Euplotes aediculatus (Ciliophora, Spirotrichea): Insights Into the Ecological Role of Antimicrobial Compounds From Environmental Bacterial Strains

Harmful Effect of Rheinheimera sp. EpRS3 (Gammaproteobacteria) Against the Protist Euplotes aediculatus (Ciliophora, Spirotrichea): Insights Into the Ecological Role of Antimicrobial Compounds From Environmental Bacterial Strains

Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics

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