Exemplar Abstract for Variovorax paradoxus (Davis et al. 1969) Willems et al. 1991.

2003 ◽  
Author(s):  
Charles Thomas Parker ◽  
Dorothea Taylor ◽  
George M Garrity
Keyword(s):  
2019 ◽  
Vol 120 ◽  
pp. 61-68 ◽  
Author(s):  
Ulrike Brandt ◽  
Gulsina Galant ◽  
Christina Meinert-Berning ◽  
Alexander Steinbüchel

2015 ◽  
Vol 81 (24) ◽  
pp. 8478-8488 ◽  
Author(s):  
Lee R. Terry ◽  
Thomas R. Kulp ◽  
Heather Wiatrowski ◽  
Laurence G. Miller ◽  
Ronald S. Oremland

ABSTRACTBacterial oxidation of arsenite [As(III)] is a well-studied and important biogeochemical pathway that directly influences the mobility and toxicity of arsenic in the environment. In contrast, little is known about microbiological oxidation of the chemically similar anion antimonite [Sb(III)]. In this study, two bacterial strains, designated IDSBO-1 and IDSBO-4, which grow on tartrate compounds and oxidize Sb(III) using either oxygen or nitrate, respectively, as a terminal electron acceptor, were isolated from contaminated mine sediments. Both isolates belonged to theComamonadaceaefamily and were 99% similar to previously described species. We identify these novel strains asHydrogenophagataeniospiralisstrain IDSBO-1 andVariovorax paradoxusstrain IDSBO-4. Both strains possess a gene with homology to theaioAgene, which encodes an As(III)-oxidase, and both oxidize As(III) aerobically, but only IDSBO-4 oxidized Sb(III) in the presence of air, while strain IDSBO-1 could achieve this via nitrate respiration. Our results suggest that expression ofaioAis not induced by Sb(III) but may be involved in Sb(III) oxidation along with an Sb(III)-specific pathway. Phylogenetic analysis of proteins encoded by theaioAgenes revealed a close sequence similarity (90%) among the two isolates and other known As(III)-oxidizing bacteria, particularlyAcidovoraxsp. strain NO1. Both isolates were capable of chemolithoautotrophic growth using As(III) as a primary electron donor, and strain IDSBO-4 exhibited incorporation of radiolabeled [14C]bicarbonate while oxidizing Sb(III) from Sb(III)-tartrate, suggesting possible Sb(III)-dependent autotrophy. Enrichment cultures produced the Sb(V) oxide mineral mopungite and lesser amounts of Sb(III)-bearing senarmontite as precipitates.


Author(s):  
Christina Meinert ◽  
Marc Schürmann ◽  
Jan-Eike Domeyer ◽  
Anja Poehlein ◽  
Rolf Daniel ◽  
...  
Keyword(s):  

2019 ◽  
Author(s):  
Richard J. Fredendall ◽  
Jenny L. Stone ◽  
Michael J. Pehl ◽  
Paul M. Orwin

ABSTRACTWe used transcriptome analysis by paired-end strand specific RNA-seq to evaluate the specific changes in gene expression associated with the transition to static biofilm growth in the rhizosphere plant growth promoting bacterium Variovorax paradoxus EPS. Triplicate biological samples of exponential growth, stationary phase, and static biofilm samples were examined. DESeq2 and Rockhopper were used to identify robust and widespread shifts in gene expression the transcriptomic signals specific to each growth phase. Weidentified 1711 protein coding genes (28%) using DESeq2 that had altered expression greater than 2-fold specifically in biofilms compared to exponential growth. Fewer genes were specifically differentially expressed in stationary phase culture (757, 12%). A small set of genes (103/6020) were differentially expressed in opposing fashions in biofilm and stationary phase, indicating potentially substantial shifts in phenotype. Gene Ontology analysis showed that the only class of genes specifically upregulated in biofilms were associated with nutrient transport, highlighting the importance of nutrient uptake in the biofilm. The biofilm specific genes did not overlap substantially with the loci identified by mutagenesis studies, although some were present in both sets. The most highly upregulated biofilm specific gene is predicted to be a part of the RNA degradosome, which indicates that RNA stability is used to regulate the biofilm phenotype. Two small putative proteins, Varpa_0407 and Varpa_3832, are highly expressed specifically in biofilms and are predicted to be secreted DNA binding proteins, that may stabilize extracellular DNA as a component of the biofilm matrix. An flp/tad type IV pilus locus (Varpa_5148-60) is strongly downregulated in specifically in biofilms, in contrast with results from other systems for these pili. Mutagenesis confirms that this locus is important in surface motility rather than biofilm formation. These experimental results suggest that V. paradoxus EPS biofilms have substantial regulatory and structural novelty.


2021 ◽  
Author(s):  
Pan Pan Wang ◽  
Li Fang Yang ◽  
Jia Ling Sun ◽  
Ye Yang ◽  
Yuan Qu ◽  
...  

Abstract Background: Panax notoginseng (Burkill) F. H. Chen is a Chinese medicinal plant of the Araliaceae family commonly used in the treatment of cardiovascular and cerebrovascular diseases in Asia and elsewhere. To meet an increase in Chinese herbal medicine market demand, most P. notoginseng is planted artificially, and is vulnerable to various plant diseases. Root rot disease, in particular, causes substantial P. notoginseng yield reduction and economic losses. High-depth next-generation sequencing technology was used to analyze the rhizosphere and root endophyte microbial communities of P. notoginseng to compare the characteristics of these two communities between healthy and root rot diseased P. notoginseng plants, and to clarify the relationship between these microbial communities and root rot disease.Results: The P. notoginseng rhizosphere microbial community was more diverse than the root endophyte community, and the difference in functional pathways between healthy and diseased P. notoginseng plants was greater in the root endophyte than in the rhizosphere communities. Multi-database annotation results showed that the highest number of endophytic bacteria occurred in the roots of diseased plants. The number of carbohydrate-active enzymes database families was also higher in diseased roots. The RND antibiotic efflux function was higher in the healthy samples. A high abundance of Variovorax paradoxus and Pseudomonas fluorescens occurred in the healthy and diseased root endophyte communities, respectively. Ilyonectria mors-panacis and Pseudopyrenochaeta lycopersici were most abundant in the diseased samples. In addition, the complete genome of two unknown Flavobacteriaceae species and one unknown Bacteroides species were obtained based on binning analysis.Conclusions: The rhizosphere and root endophyte microbial communities of healthy and root rot diseased P. notoginseng showed marked differences in diversity and functional pathways. The higher mapping values obtained for the diseased samples reflected the occurrence of root rot disease at the molecular level. Variovorax paradoxus and Pseudomonas fluorescens may be antagonistic bacteria of root rot in P. notoginseng, whereas Ilyonectria mors-panacis and Pseudopyrenochaeta lycopersici appear to be P. notoginseng root rot pathogens. Our study provides a theoretical basis for understanding the occurrence of root rot in P. notoginseng and for further research on potential biological control agents.


Author(s):  
A. A. Belimov ◽  
◽  
A. I. Shaposhnikov ◽  
D. S. Syrova ◽  
T. S. Azarova ◽  
...  

The aim of our research was to study the effect of growth-promoting rhizobacteria (Pseudomonas oryzihabitans and Variovorax paradoxus) and toxic elements (Al, Cd and Hg) on the root exudation in various pea (Pisum sativum L.) genotypes. For this, methods of periodic cultures, gnotobiotic plant-microbial systems, ICPE and UPLC were used. It was established that rhizobacteria actively utilized organic acids and sugars secreted by the roots and contributed to an increase in pH and Al immobilization in the rhizosphere. Cadmium increased the exudation of many substances of pea line SGE, but this effect was more pronounced in the mutant SGECdt. Stimulation of the exudation of amino acids was detected during Hg treatment to a greater extent in wild-type SGE. The combined action of Cd and Hg did not lead to a further increase in exudation. The results obtained indicate various mechanisms of exudation of the studied fractions, while the most pronounced differences are observed between the fractions of amino acids or sugars with organic acids. Exudation of organic acids plays an important role in the decreased stability and accumulation of Hg by the pea mutant SGECdt.


2021 ◽  
Author(s):  
Isiri Adhiwarie Perera ◽  
Sudharsanam Abinandan ◽  
Suresh R. Subashchandrabose ◽  
Kadiyala Venkateswarlu ◽  
Ravi Naidu ◽  
...  

2000 ◽  
Vol 182 (24) ◽  
pp. 6921-6926 ◽  
Author(s):  
Jared R. Leadbetter ◽  
E. P. Greenberg

ABSTRACT Acyl-homoserine lactones (acyl-HSLs) serve as dedicated cell-to-cell signaling molecules in many species of the classProteobacteria. We have addressed the question of whether these compounds can be degraded biologically. A motile, rod-shaped bacterium was isolated from soil based upon its ability to utilizeN-(3-oxohexanoyl)-l-homoserine lactone as the sole source of energy and nitrogen. The bacterium was classified as a strain of Variovorax paradoxus. TheV. paradoxus isolate was capable of growth on all of the acyl-HSLs tested. The molar growth yields correlated with the length of the acyl group. HSL, a product of acyl-HSL metabolism, was used as a nitrogen source, but not as an energy source. Cleavage and partial mineralization of the HSL ring were demonstrated by using radiolabeled substrate. This study indicates that some strains of V. paradoxus degrade and grow on acyl-HSL signals as the sole energy and nitrogen sources. This study provides clues about the metabolic pathway of acyl-HSL degradation by V. paradoxus.


2017 ◽  
Vol 5 (36) ◽  
Author(s):  
Chi Eun Hong ◽  
Sung Hee Jo ◽  
Ick-Hyun Jo ◽  
Haeyoung Jeong ◽  
Jeong Mee Park

ABSTRACT Variovorax paradoxus KB5, isolated from the inside of Arabidopsis thaliana leaves, showed antibacterial activity against the phytopathogen Pseudomonas syringae pv. tomato DC3000. Here, we report a draft genome sequence of V. paradoxus KB5, which contains a delftibactin-like nonribosomal peptide biosynthetic gene cluster.


2019 ◽  
Vol 8 (3) ◽  
pp. 312 ◽  
Author(s):  
Hye Han ◽  
Sun-Young Lee ◽  
Seo Oh ◽  
Hee Moon ◽  
Hyunseok Cho ◽  
...  

Mucosal inflammation is characterized by neutrophil and mononuclear cell infiltration. This study aimed to determine the gastric and duodenal microbiota associated with histological, endoscopic, and symptomatic gastritis. Dyspeptic adults who presented for evaluation were included. Subjects with either comorbidities or recent drug intake were excluded. Three endoscopic biopsies were obtained from the antrum, body, and duodenum. Next-generation sequencing for 16S ribosomal RNA V1–V2 hypervariable regions was performed. The correlation between the composition of microbiota and the degree of inflammatory cell infiltration, endoscopic findings, and Patient Assessment of Gastrointestinal Disorders Symptom Severity Index (PAGI-SYM) score was analyzed. In 98 included subjects, microbial communities in the antrum and body showed Bray–Curtis similarity; however, those in the duodenum showed dissimilarity. Histological and endoscopic gastritis was associated with the abundance of Helicobacter pylori and that of commensal bacteria in the stomach. The abundances of Variovorax paradoxus and Porphyromonas gingivalis were correlated with histological gastritis, but not with endoscopic or symptomatic gastritis. The total PAGI-SYM score showed a stronger correlation with the duodenal microbiota (Prevotella nanceiensis and Alloprevotella rava) than with the gastric microbiota (H. pylori, Neisseria elongate, and Corynebacterium segmentosum). Different correlations of the gastric and duodenal microbiota with histological, endoscopic, and symptomatic gastritis were observed for the first time at the species level. H. pylori-negative gastritis is not associated with endoscopic or symptomatic gastritis. Only H. pylori-induced endoscopic gastritis requires gastric cancer surveillance. Owing to the weak correlation with H. pylori, symptomatic gastritis should be assessed separately from histological and endoscopic gastritis.


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