Computational prediction of microRNAs in marine bacteria of the genus Thalassospira.

MicroRNAs (miRNAs) are key players in regulation of gene expression at post-transcription level in eukaryotic cells. MiRNAs have been intensively studied in plants, animals and viruses. The investigations of bacterial miRNAs have gained less attention, except for the recent studies on miRNAs derived from Streptococcus mutans ATCC 25175 and Escherichia coli DH10B. In this study, high-throughput sequencing approach was employed to investigate the miRNA population in bacteria of the genus Thalassospira using both the miRDeep2 and CID-miRNA methods. A total of 984 putative miRNAs were identified in 9 species of the genus Thalassospira using both miRDeep and CID-miRNA analyses. Fifty seven conserved putative miRNAs were found in different species of the genus Thalassospira, and up to 6 miRNAs were found to be present at different locations in the T. alkalitolerans JCM 18968T, T. lucentensis QMT2T and T. xianhensis P-4T. None of the putative miRNAs was found to share sequence to the reported miRNAs in E. coli DH10B and S. mutans ATCC 25175. The findings provide a comprehensive list of computationally identified miRNAs in 9 bacterial species of the genus Thalassospira and addressed the existing knowledge gap on the presence of miRNAs in the Thalassospira genomes.

Thalassospira australica sp. nov. isolated from sea water.

Two Gram-negative, non-pigmented, motile bacteria were isolated from a sea water sample collected at St. Kilda Beach, Port Philip Bay, Victoria, Australia. The two strains were found to grow between 4 and 40 °C, pH 5-10 and tolerate up to 10 % NaCl. A phylogenetic study, based on a 16S rRNA gene sequence analysis indicated that strains NP 3b2(T) and H 94 belong to the genus Thalassospira. The sequence similarity of the 16S rRNA gene between the two new isolates is 99.8 % and between these strains and all validly named Thalassospira species was found to be in the range of 95-99.4 %. The DNA-DNA relatedness between the two strains was found to be 80.2 %, while relatedness with other validly named species of the genus Thalassospira was between 53 and 65 %. The average nucleotide identity (ANI) and the in silico genome-to-genome distance (GGD) between the two bacteria and T. profundimaris WP0211(T), T. xiamenensis M-5(T), 'T. permensis' NBRC 106175(T) and T. lucentensis QMT2(T) was 76-82 % and 21-25 %, respectively. The results of phylogenetic and genomic analysis, together with physiological and biochemical properties, indicated that the two strains represent a new species of the genus Thalassospira. Based on these data, a new species, Thalassospira australica, is proposed with strain NP 3b2(T) (=KMM 6365(T) = JCM 31222(T)) as the type strain.