Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA

• Published in: BMC genomics Vol. 17; no. 83; p. 93
• Main Authors: García-Romero, Inmaculada, Pérez-Pulido, Antonio J, González-Flores, Yolanda Elisabet, Reyes-Ramírez, Francisca, Santero, Eduardo, Floriano, Belén
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 04.02.2016; BioMed Central
• Subjects: Analysis; Bacteriophages - physiology; Biological diversity; Chromosomes, Bacterial; Computational Biology; Gene Transfer, Horizontal; Genetic aspects; Genome, Bacterial; Genomic Islands; Genomics; High-Throughput Nucleotide Sequencing; Nitrates - metabolism; Phylogeny; Proteobacteria; Proteome; Proteomics - methods; RNA sequencing; Secondary Metabolism; Sequence Analysis, DNA; Sphingomonas - genetics; Sphingomonas - metabolism; Sphingomonas - virology
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-016-2411-1

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. 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. 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.