ArticleBMC genomics2016
Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 53 citations in OpenAlex.
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- Potential of stable isotope analysis to deduce anaerobic biodegradation of ethyl tert-butyl ether (ETBE) and tert-butyl alcohol (TBA) in groundwater: a review.Environmental science and pollution research international · 2024Review
- An improved genome editing system for Sphingomonadaceae.Access microbiology · 2024Article
- Temporal stability and community assembly mechanisms in healthy broiler cecum.Frontiers in microbiology · 2023Article
- The functional differences between paralogous regulators define the control of the general stress response in Sphingopyxis granuli TFA.Environmental microbiology · 2022Article
- Characteristics of denitrification and microbial community in respect to various HFrontiers in microbiology · 2022Article
- Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration.Animal microbiome · 2021Article
- Identification of two fnr genes and characterisation of their role in the anaerobic switch in Sphingopyxis granuli strain TFA.Scientific reports · 2020Article
- Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling.Scientific reports · 2020Article
- Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA.Scientific reports · 2020Article
- Genome-Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation ofBioMed research international · 2020Article
- Article
- Review
- The response of Sphingopyxis granuli strain TFA to the hostile anoxic condition.Scientific reports · 2019Article
- Adaptive Evolution ofFrontiers in microbiology · 2019Article
- Article
- Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales.Microbial genomics · 2018Article
- Performance and microbial characteristics of biomass in a full-scale aerobic granular sludge wastewater treatment plant.Environmental science and pollution research international · 2018Article
- The first characterized phage against a member of the ecologically important sphingomonads reveals high dissimilarity against all other known phages.Scientific reports · 2017Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSphingomonads are Alphaproteobacteria that belong to the Sphingomonas, Novosphingobium, Sphingopyxis or Sphingobium genera, They are physiologically diverse and broadly distributed in nature, playing important roles in oligotrophic environments and in the degradation of recalcitrant polyaromatic compounds, Sphingopyxis is a poorly studied genus of which only one representative (S. alaskensis RB2256) has been deeply characterized. In this paper we analyze the genomic features of S. granuli strain TFA (formerly Sphingomonas macrogoltabida) in comparison with the available Sphingopyxis sequenced genomes, to describe common characteristics of this genus and to highlight unique characteristics of strain TFA.
resultsThe TFA genome has been assembled in a single circular chromosome of 4.7 Mb. Genomic sequence analysis and proteome comparison re-assigned the TFA strain to the Sphingopyxis genus and the S. granuli species. Some regions of the TFA genome show high similarity (ca. 100%) to other bacteria and several genomic islands have been detected. Pathways for aromatic compound degradation have been predicted but no growth of TFA has been detected using these as carbon or nitrogen sources. Genes for nitrate respiration have been identified as TFA exclusive. Experimental data on anaerobic growth of TFA using nitrate as a terminal electron acceptor are also provided.
conclusionsSphingopyxis representatives form a compact phylogenetic group (with the exception of S. baekryungensis DSM 16222) that share several characteristics, such as being naturally resistant to streptomycin, having only one ribosomal operon, a low number of prophages and CRISPR sequences, absence of selenoproteins and presence of ectoin and other biosynthesis pathways for secondary metabolites. Moreover, the TFA genome organization shows evidence of the presence of putative integrative and conjugative elements (ICE) responsible for the acquisition of several characteristics by horizontal transfer mechanisms. Sphingopyxis representatives have been described as strict aerobes but anaerobic growth using nitrate as a terminal electron acceptor might confer an environmental advantage to the first S. granuli strain characterized at genomic level.
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