title: Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA.
abstract: BACKGROUND
  Sphingomonads 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.
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  Sphingopyxis 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.
authors: Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013, Seville, Spain. igarrom@upo.es.
authors: Inmaculada
authors: I
authors: García-Romero
authors: Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013, Seville, Spain. ajperez@upo.es.
authors: Antonio J
authors: AJ
authors: Pérez-Pulido
authors: Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013, Seville, Spain. yegonflo@upo.es.
authors: Yolanda Elisabet
authors: YE
authors: González-Flores
authors: Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013, Seville, Spain. freyram@upo.es.
authors: Francisca
authors: F
authors: Reyes-Ramírez
authors: Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013, Seville, Spain. esansan@upo.es.
authors: Eduardo
authors: E
authors: Santero
authors: Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, ES-41013, Seville, Spain. bflopar@upo.es.
authors: Belén
authors: B
authors: Floriano
mesh_terms: D001435:Bacteriophages / Q000502:physiology; D002876:Chromosomes, Bacterial; D019295:Computational Biology; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D009566:Nitrates / Q000378:metabolism; D010802:Phylogeny; D020543:Proteome; D040901:Proteomics / Q000379:methods; D064210:Secondary Metabolism; D017422:Sequence Analysis, DNA; D020578:Sphingomonas / Q000235:genetics* / Q000378:metabolism / Q000821:virology
chemical_list: D009566:Nitrates; D020543:Proteome