Genomic characteristics and polyphasic taxonomy of strain IMCC13023, actinorhodopsin-containing bacterium, isolated from Arctic seawter

초록

It has been known that a part of marine actinobacterial populations are closely related to several freshwater lineages of the Actinobacteria. However, studies on those marine actinobacterial clusters including the Luna groups have been hampered by the lack of relevant isolates. Here we present the polyphasic taxonomy and genome characteristics of strain IMCC13023 that was isolated from a coastal Arctic seawater sample collected off the coast of the Dasan station, located in Svalbard, Norway during the glacier melting season. Strain IMCC13023 was closely related (up to 98.4% 16S rRNA gene sequence similarity) to members of the Luna1-A1 clade containing ‘Candidatus Aquiluna rubra’, an abundant freshwater actinobacterial lineage. Pyrosequencing of 16S rRNA genes showed that IMCC13023-related marine bacteria comprised a significant portion (4.7-21.1%) of the bacterial community of the Arctic seawater samples. Cells of strain IMCC13023 were Gram-staining positive, strictly aerobic curved rods that contain orange-to-red pigments. Optimal growth of the strain was observed at 15℃, pH 7-8, and in the presence of 1% NaCl. The major fatty acid (>10%) were anteiso-C15:0(24.2%), iso-C15:0(19.4%), C16:0(13.0%), iso-C16:0(11.8%) and major polar lipids were phosphatidylglycerol and diphosphatidylglycerol, which differentiated the strain from other genera in the Actinobacteria. Illumina sequencing followed by combinatorial PCR yielded the complete genome sequence of 1.36Mb, the smallest genome size ever reported among free-living actinobacteria, with G+C content of 51.7 mol%, 1371 CDS, 3 rRNA, 43 tRNA. A rhodopsin gene found in the genome was affiliated with actinorhodopsin and the amino acid sequence of IMCC13023 actinorhodopsin was closely related (~80%) to that of ‘Candidatus Aquiluna rubra’. Maximum absorption spectral peak of the actinorhodopsin was found at 524 nm when the gene was expressed in Escherichia coli. Amino acid-residue and biophysical analysis of the actinorho