Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle

Abstract

BackgroundPontimonas salivibrio strain CL-TW6T (=KCCM 90105 = JCM18206) was characterized as the type strain of a new genus within the Actinobacterial family Microbacteriaceae. It was isolated from a coastal marine environment in which members of Microbactericeae have not been previously characterized.ResultsThe genome of P. salivibrio CL-TW6T was a single chromosome of 1,760,810 bp. Genomes of this small size are typically found in bacteria growing slowly in oligotrophic zones and said to be streamlined. Phylogenetic analysis showed it to represent a lineage originating in the Microbacteriaceae radiation occurring before the snowball Earth glaciations, and to have a closer relationship with some streamlined bacteria known through metagenomic data. Several genomic characteristics typical of streamlined bacteria are found: %G + C is lower than non-streamlined members of the phylum; there are a minimal number of rRNA and tRNA genes, fewer paralogs in most gene families, and only two sigma factors; there is a noticeable absence of some nonessential metabolic pathways, including polyketide synthesis and catabolism of some amino acids. There was no indication of any phage genes or plasmids, however, a system of active insertion elements was present. P. salivibrio appears to be unusual in having polyrhamnose-based cell wall oligosaccharides instead of mycolic acid or teichoic acid-based oligosaccharides. Oddly, it conducts sulfate assimilation apparently for sulfating cell wall components, but not for synthesizing amino acids. One gene family it has more of, rather than fewer of, are toxin/antitoxin systems, which are thought to down-regulate growth during nutrient deprivation or other stressful conditions.ConclusionsBecause of the relatively small number of paralogs and its relationship to the heavily characterized Mycobacterium tuberculosis, we were able to heavily annotate the genome of P. salivibrio CL-TW6T. Its streamlined status and relationship to streamlined metagenomic constructs makes it an important reference genome for study of the streamlining concept. The final evolutionary trajectory of CL-TW6 T was to adapt to growth in a non-oligotrophic coastal zone. To understand that adaptive process, we give a thorough accounting of gene content, contrasting with both oligotrophic streamlined bacteria and large genome bacteria, and distinguishing between genes derived by vertical and horizontal descent.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5019-9) contains supplementary material, which is available to authorized users.

Spatio-Temporal Variation of the Bacterial Communities along a Salinity Gradient within a Thalassohaline Environment (Saline di Tarquinia Salterns, Italy)

“…This genus includes only one species ( P. salivibrio ) and the only cultivable strain (CL-TW6) was isolated in Korea from a solar saltern pond showing salinity slightly higher than seawater. It was assumed to be a slightly halophilic marine bacterium (optimal growth at 30‰ of salinity) by the researchers that described the species [ 58 , 59 ], who supposed that it was drawn into the saltern from the coastal environment [ 60 ]. No other work reports isolation of P ontimonas strains from MS or other hypersaline environments.…”

Analysis of Different Size Fractions Provides a More Complete Perspective of Viral Diversity in a Freshwater Embayment

“…The Pontimonas genus contains only one described strain, Pontimonas salivibrio strain CL-TW6 T , which was recently isolated from a coastal marine environment along with its virus and was hypothesized to occupy environments that experience significant stresses (57), such as Hamilton Harbour. The researchers concluded that its lytic virus was poorly adapted to replicate in this strain, since repeated attempts to sequence its genome were unsuccessful.…”

Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification

“…In order to explore the distribution of HD-domain dNTPases in prokaryotes, we made use of the library of proteins from completely sequenced bacterial genomes (February 2018 version) described in 87 , and local implementations of the BLAST toolkit 88 , the HHpred system 89 , the UCSC Sequence Analysis and Alignment system 90 , PAUP ( https://paup.phylosolutions.com ), and MrBayes 3.2.7 91 . The library is formatted to contain protein accession, nucleotide accession, and full taxonomic distribution on each protein sequence definition line, making it possible to directly examine the distribution within genomes and taxons of any clade found within the library.…”