Complete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River Water

Abstract

Aurantimicrobium minutum type strain KNC^T is a planktonic ultramicrobacterium isolated from river water in western Japan. Strain KNC^T has an extremely small, streamlined genome of 1,622,386 bp comprising 1,575 protein-coding sequences. The genome annotation suggests that strain KNC^T has an actinorhodopsin-based photometabolism.

GENOME ANNOUNCEMENT

The phylum Actinobacteria includes members that are often numerically dominant (up to 60%) in the freshwater bacterial communities (1, 2). The actinobacterial Luna2 lineage, currently classified into the acIII lineage (2), has a cosmopolitan distribution in inland freshwater ecosystems (3). The cell morphology of this lineage is typical of ultramicrobacteria (cell volume <0.1 µm³ [4]). Aurantimicrobium minutum type strain KNC^T was the first described strain with a validly published name within the acIII lineage of Actinobacteria (5) and was isolated from a 0.2 µm filtrate of river water in western Japan (6). Here, we report the whole-genome sequence of strain KNC^T, with the aim of elucidating the physiological traits that have facilitated such a wide distribution pattern.

The genomic DNA of strain KNC^T was extracted from cells grown in nutrient broth, soytone, yeast extract (NSY) liquid medium (7) using Qiagen Genomic-Tip 100/G columns. Genomic shotgun and fosmid-end sequences were determined using an ABI3730xl sequencer. De novo assembly was conducted with phrap version 1.080812, resulting in a single chromosome with 22.2-fold genome coverage. The total length of the complete genome was 1,622,386 bp with a G+C content of 52.8 mol%. Strain KNC^T has an extremely small, streamlined genome that is consistent with other ultramicrobacteria such as “Candidatus Pelagibacter ubique” (8) (Alphaproteobacteria) and Rhodoluna lacicola (9) (Actinobacteria). The phylum Actinobacteria is generally considered to be comprised of high-G+C Gram-positive bacteria. However, the genomes of freshwater and marine actinobacteria were recently reported to have unusually low G+C contents (9, 10). The genomic G+C content of freshwater strain KNC^T is also quite low.

The genome annotation by the Microbial Genome Annotation Pipeline online server (11) predicted one copy of 16S-23S-5S rRNA operon, 42 tRNAs, and 1,575 protein-coding sequences. The genome encoded a putative rhodopsin, known as actinorhodopsin (12), suggesting that strain KNC^T has an ability to utilize light energy for supplemental energy generation. Conversely, genes encoding a cytochrome bd complex, a respiratory quinol:O₂ oxidoreductase found in many prokaryotes and expressed under oxygen-limited conditions (13), were missing within the genome. Comparative genomic analysis by MBGD (14) revealed that the genomic traits described above are shared with the genome of another ultramicrosized actinobacterium R. lacicola (9). In summary, we sequenced the complete genome of a cosmopolitan freshwater ultramicrobacterium. This will provide new insight into genome streamlining and related missing genes of ultramicrobacteria.

Nucleotide sequence accession number.

The complete genome sequence of A. minutum KNC^T has been deposited in the DDBJ/ENA/GenBank database under the accession no. AP017457. Annotated genome data were deposited with the help of the Genome Refine web service (http://genome.annotation.jp/genomerefine/).