Bacterial Diversity Of Qucai Hot Springs In Tibet & Comparative Genomics Of The Genus Thermus

Terrestrial hot springs are special habitats for thermophilic microorganisms.The present study was designed to study and understand the bacterial community structure of hot springs in Naqu County in Tibet,China by using culture-independent method and culture dependent method.In addition,a phylogenomics study of genus Thermus from Qucai hot springs in Tibet and Tengchong hot springs in Yunnan was also performed to unravel the genomic diversity among the strains of Thermus species as well its adaptability strategy in geographically two different locations.The culture-independent study was used to screen 38 phyla,80 classes,154 orders,302 families and 789 genera from 11 samples that were collected from Qucai hot springs in Tibet.At the phylum level,the predominant groups were Proteobacteria,Firmicutes and Bacteroidetes.A deeper characterization of the bacterial community structure revealed the presence of several heterotrophic groups comprised of Pseudomonas,Symbiobacterium,Brevundimonas,Thiobacillus,Thermus and Paenibacillus and others.The effect of samples temperature on bacterial community composition of the culture-independent study was also investigated.The relative abundance of the bacterial community showed a negative correlation with temperature because high-temperature samples showed less diversity.Low abundance of bacterial phyla including,Bacteroidetes,Deinococcus-Thermus,Cyanobacteria and Chloroflexi were observed in samples having a temperature above 80 °C.In a study of Culture-dependent technique,four different isolation media were used for isolation of thermophilic bacterial strains from 11 samples of Qucai hot springs.Total,220 bacterial strains were obtained and identified,representing 3 phyla,4 classes,7 orders,12 families and 22 genera and including two potential new genera and six new species.The most dominant phyla were Firmicutes,Deinococcus-Thermus and Proteobacteria.At the genus level,Geobacillus was dominant followed by Thermus.The effect of T5 medium resulted in isolating many Thermus strains.We also sequenced the genomes of 17 Thermus strains,isolated from Qucai hot springs in Tibet and Tengchong hot springs in Yunnan and performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenomic relationship and genomic diversity of strains belonging to same species from different geographical locations,we compared 17 genomes with 21 reference Thermus genomes to assess their phylogenetic relationships based on 16 S rRNA gene sequences by supermatrix and by gene content methods.Phylogenomic analyses revealed a mixed distribution of the strains,which was uncoupled from their geographical origin.These results suggested that geography has no effect on Thermus genomes.Our findings revealed the absence of specific genomic signatures marking adaptations of Thermus strains towards two different locations.This suggests fundamentally similar trends of adaptability of genus Thermus in a high-temperature environment.Although the genome of different strains belongs to same species were highly similar,but subtle differences were found.For example,genes encoding Metalloproteinase were detected in the genomes of Thermus antranikianii species isolated from Tengchong hot spring.Genome-wide screening CRISPR loci libraries were identified.The comparative analysis showed the presence of competence loci across all the Thermus genomes analysed.These data suggested that Thermus species from both locations had well developed defense system against viruses and adopt similar strategy for survival.Analysis of the seventeen Thermus genomes also revealed that these encode pathways for the synthesis of secondary metabolites(isoprenoid),pigments(carotenoid),folates and heme.These have attracted industrial interest for application in food industries and medical field.The CRISPR/Cas system that is found in Thermus could be an interesting tool in molecular biology,particularly for genome editing.