Pan-genomics Study Of Marine Environmental Adaptation Mechanisms Of Streptomyces

The development of sequencing technology and decreasing of sequencing cost make more and more bacterial genomes are available. The accumulation of these bacterial genome data leads microbiologists find that great diversity exists even in the same bacterial species and that the genome of a single strain can not represent a species. Since the conception of pan-genome was proposed in 2005, it provide a new method to study bacterial species diversity, evolution, adaptability, population structure, vaccine design or virulence gene identification, and so on. As an extension of comparative genomics, pan-genomics provides a very good method to explore the commonness and specifity of genomes between diffetent strains. So we use this method to study the mechanism of marine environmental adaptation of Streptomycs.In this study,9 Streptomyces strains, isolated from different Longitude, latitude and depth of marine sediment or gorgonian of the South China Sea, are sequenced. The pan-genomics analysis, phylogenetic analysis, and comparative analysis of these strains and 22 relative strains downloaded from National Center for Biotechnology Information (NCBI) are performed to reveal the mechanism of marine environmental adaptation of Streptomycs. Firstly, the results of pan-genomics analysis suggest that Streptomycs have an open pan-genome, which is in consistent with the diversity of their living habitat. According to the phylogenetic analysis based on single copy core genes, these 31 strains can be divided into two groups. One group is called the marine source group, containing 17 strains isolated from marine and the remaining one is isolated from human beings. The other group is called multiple source group with 13 strains which are isolated from many different environments, such as marine, soil, insect, plant, and so on. Comparing the differences between the two groups got following results. First, gene gain and loss study indicate that both groups gained a lot of genes in the initial period of evolution, and the ancestor of multiple source group gained more (about 6/7) genes than the ancestor of the other group, which lead the former with bigger genomes; Second, sequence identity comparison of single copy core genes among or between strains of these two groups shows that marine source strains with a lower sequence identity, implying there are larger divergence between these genomes; Third, Clusters of Orthologous Groups (COG) functional enrichment analysis indicates that strains from marine source group accumulated more genes with functions of translation, ribosomal structure and biogenesis as well as posttranslational modification, protein turnover, and chaperones, which may help protein folding and maintaining stability under low temperature and high tension conditions; Four, according to the classification of transporter family in Transporter Protein Analysis Database (TransportDB), strains of marine source group have more transporter families involved in adapting to osmotic pressure, low temperature, oligotrophic and other marine specific conditions; Five, the results of signal transduction system comparison of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway suggest that strains of marine source group accumulated more systems involved in making full use of nutrients under oligotrophic condition, such as Two-component system of phosphate assimilation, galactose oligomer/maltooligosaccharide ATP-binding cassette (ABC) transporter, multiple sugar ABC transporter and L-asorbate phosphotransferase system (PTS). Finally, considering the large variety of virus in marine environment, reaching 5～10 times of the number of bacteria, it is not surprising that strains isolated from marine environment contain more Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs), which are involved in antiphage function with the mechanism like RNA silence.This study shows that marine Streptomyces accumulate more functional genes, transporters, and metabolic pathways to adapt to low temperature, high tension, and oligotrophic marine conditions; and marine Streptomyces also with more CRISPRs to resistance to phage. Therefore, pan-genomics is a very effective method to study the mechanism of environmental adaptation of microorganisms.