The Biological Characteristics Of Mineral Weathering Bacteria And Complete Genome Analysis Of Dyella Jiangningensis SBZ3-12

Microorganisms play important role in the rock weathering,mineral dissolution and the metal recycling.Despite decades of dedicated efforts by many scholars,controversies remain regarding the roles of microorganisms in mineral precipitation and weathering and the molecular mechanism behind the bio-degradation,especially lack of the knowledge of genome of mineral weathering bacteria.Bacteria can weather mineral by means of generating biofilms,organic acids,siderophore,and so on.This study tested the biological characteristics of 4 mineral weathering bacteria,and chose the mineral weathering bacterium Dyella jiangningensis SBZ3-12 as the research object.We studied the genetic background of mineral weathering bacterium by means of complete genome sequence and comparative genomic analysis.The genome was sequenced by use of 454 GS Junior pyrosequencing,it yielded 373,571 reads,and these reads were assembled into 39 large contigs using the Newbler 2.4 assembly software program.Gap-filling was conducted by PCR amplification.Genome analysis found that the strain D.jiangningensis SBZ3-12 genome total length was 5,396,991 bp,GC content was 64.22%.It has 4,790 genes,25 pseudogenes,6 rRNAs,52 tRNAs and one ncRNA.Genome predicted ORFs were submitted to the online data base such as COG,VFDB,PA1DB,ARDB and KEGG to classification and annotation functions.The COG analysis shows that the number of COG class "R" is the most accounted for 9.39%of the total CDs;the second is class"E" accounted for 6.15%of the total CDs.The VFDB analysis shows that there are 137 potential virulence genes accounted for 2.94%of the total CDs.The ARDB analysis shows that there are 9 potential drug resistance genes including those resistant to chloramphenicol,macrolide,trimethoprim,kasugamycin and fosmidomycin.The potential horizontal transferring elements analysis shows that there are 1,068 potential horizontal transferring genes about accounted for 22.89%of the total CDs.Among these potential horizontal transferring genes,86.70%were putatively derived from plasmids,12.73%were from prophages and 0.57%from viruses.Comparative genomics,such as basic metabolism and synteny,were carried out.The results show that there is a good linear relation between strain D.jiangningensis SBZ3-12 and strain D.japonica A8.The metabolic pathways show that strain D.jiangningensis SBZ3-12 has the complete TCA cycle,while the TCA cycle of the other genera of Dyella is not complete.The genome analysis shows that it has the catecholate siderophore receptor that may be involved in the pyoverdine-type siderophore transport.In order to analysis the structure of CsrA,we submitted the CsrA sequences to the online data base such as ExPASy ProtParam Server,Pole Bioinformatique Lyonnais Network Protein sequence analysis and SWISS-MODEL.Although there is no obvious difference in the primary sequence,their advanced structure is significantly different because of the different functions of CsrA in different strains.The results may help us to understand the molecular mechanism of mineral weathering better.Based on phenotypic,chemotaxonomic and phylogenetic analysis,strain A31 represents a novel species of the genus Sinomonas,for which the name Sinomonas susongensis sp.nov.is proposed.