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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2411-1) contains supplementary material, which is available to authorized users.
Highlights
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
The genome size of Sphingopyxis representatives ranges from ca. 3 Mb of S. baekryungensis DSM 16222 to ca. 4.9 Mb of S. fribergensis Kp5.2
The GC content is higher than 60 % in all sequenced Sphingopyxis and only two of them, S. alaskensis RB2256 and S. fribergensis Kp5.2, bear free plasmids (28 and 208 Kb, respectively)
Summary
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. Sphingomonads have been described as a bacterial group within the Sphingomonadaceae Family that comprises physiologically diverse α-proteobacteria [1] Their members are classified into four different genera, Sphingomonas, Novosphingobium, Sphingopyxis and Sphingobium [2]. They have attracted attention mainly because of their metabolic diversity, which includes their capacity for xenobiotic degradation as one of the most important characteristics, and their ubiquity, as they have been isolated from many different environments. Some members of this group have been described as oligotrophic bacteria which play an important role in marine environments [3]. These studies have provided genomic features to describe oligotrophic bacteria [4], have highlighted the diversity in their genome organization [5] and defined genes involved in the quorum sensing metabolism, marine adaptation and bioremediation in the well-known Novosphingobium genus [6]
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