矿物风化细菌的生物学特性和Dyella jiangningensis SBZ3-12全基因组分析

发布时间：2018-09-16 21:53

【摘要】：微生物在矿物风化这一地质作用过程中起着重要的作用,尽管国内外学者对微生物风化矿物研究多年,对其风化矿物的机理有一定的认识,但是对于微生物在矿物风化过程中的分子生物学机制还没有统一的认识,特别是从矿物风化细菌基因组学角度研究其矿物风化作用的研究还比较欠缺。矿物风化细菌可以通过产生生物膜、有机酸和铁载体等实现对矿石的风化。本文从4株矿物风化菌株出发,测定了其和矿物风化相关的生物学特性,并以菌株D.jiangningensiS BZ3-12为研究对象,通过对其全基因组测序,利用比较基因组的分析方法,对其基因组进行分析,从基因水平阐述该菌株的遗传特征,为后续研究其风化矿物的分子生物学机制提供遗传学背景。采用454 GS Junior pyrosequencing system(Roche)测序平台对供试菌株进行全基因组测序。共获得373571条Reads,将这些Reads通过Newbler 2.4拼接得到39个Contigs,测序产生的Gap通过PCR扩增的方法补平。基因组分析发现,供试菌株D.jiangningensis SBZ3-12基因组序列总长度为5396991 bp,GC含量为64.22%,共含有4790个基因,25个假基因、6种rRNA操纵子、52种tRNA和1个ncRNA。将基因组ORF采用在线数据库COG、VFDB、PAIDB、ARDB和KEGG对其进行功能分类与注释。对菌株D.jiangningensis SBZ3-12基因组COG分析发现,COG类别为 "R"(General function prediction only)的比例最高,为 9.39%,其次为 "E"(Amino acid transport and metabolism),为6.15%;对毒力基因分析发现其基因组中含有137个潜在的毒力基因,占到所有蛋白编码序列的2.94%:对抗生素抗性基因分析发现了9个潜在的抗生素抗性基因,可能对氯霉素、大环内脂、三甲氧苄二氨嘧啶、春雷霉素和磷胺霉素具抗性;对潜在的水平转移基因分析发现共有1068个潜在的水平转移基因,占所有蛋白编码序列的22.89%,其中来源于质粒的水平转移基因、来源于原噬菌体的水平转移基因和来源于病毒的水平转移基因分别占所有水平转移基因的86.70%、12.73%和0.57%。基因组共线性分析发现菌株D.jiangningensis SBZ3-12和同属的全基因组测序菌株基因组染色体之间局部具有一定的共线性关系。对其代谢途径分析发现具有完整的TCA循环途径,能够保证苹果酸的产生。代谢途径比较分析发现Dyella属其他菌株的TCA循环途径都不完整。对其基因组分析发现含有编码儿茶酚型铁载体受体的基因,可能参与混合型铁载体的转运。通过 ExPASy ProtParam Server、Pole Bioinformatique Lyonnais Network Protein sequence analysis 和 SWISS-MODEL 在线数据库对菌株D.jiangningensi.sSBZ3-12 及其他种属的CsrA(Carbon storage regulator)分析发现,CsrA虽然一级结构差异不明显,但是其三级结构却明显不同,可能在不同菌株中行使特定的功能,为阐明该菌风化矿物的分子生物学机制奠定了基础。通过多相分类学方法鉴定一株矿物风化细菌A31为Sinomonas属的一个新种,命名为 Sinomonas susongensis sp.nov.
[Abstract]:Microbes play an important role in the geological process of mineral weathering. Although scholars at home and abroad have been studying microbial weathering minerals for many years, they have a certain understanding of the mechanism of weathering minerals. However, there is no unified understanding of the molecular biological mechanism of microorganisms in the process of mineral weathering, especially the study of its mineral weathering from the point of view of mineral weathering bacteria genomics. Mineral weathering bacteria can be weathered by biofilms, organic acids and iron carriers. In this paper, the biological characteristics related to mineral weathering of four mineral weathering strains were determined. The D.jiangningensiS BZ3-12 strain was taken as the research object, the whole genome was sequenced, and the comparative genome analysis method was used. The genetic characteristics of the strain were analyzed at the gene level, which provided the genetic background for further study on the molecular biological mechanism of the weathered minerals. The whole genome of the tested strains was sequenced by 454 GS Junior pyrosequencing system (Roche) sequencing platform. A total of 373571 Reads, fragments were obtained by Newbler 2.4 splicing to obtain 39 Contigs, sequenced Gap, which was flattened by PCR amplification. Genomic analysis showed that the total length of D.jiangningensis SBZ3-12 genomic sequence was 64.22 bp,GC, which contained 4790 genes, 25 pseudogenes, 6 rRNA operons, 52 tRNA and 1 ncRNA.. The genome ORF was classified and annotated by online database COG,VFDB,PAIDB,ARDB and KEGG. The proportion of "R" (General function prediction only) was the highest (9.39%), followed by "E" (Amino acid transport and metabolism), (6.15%). The virulence gene analysis revealed 137 potential virulence genes in the genome. 9 potential antibiotic resistance genes were found in the analysis of antibiotic resistance genes, which may be resistant to chloramphenicol, macrolipids, trimethoprim, vermicycin and fosfomycin. The analysis of potential horizontal transfer genes revealed that there were 1068 potential horizontal transfer genes, accounting for 22.89 percent of all the protein coding sequences, among which the horizontal transfer genes were derived from plasmids. Horizontal transfer genes derived from prophage and virus accounted for 86.70% and 0.57% of all horizontal transfer genes, respectively. It was found that there was a local collinear relationship between the genomic chromosomes of D.jiangningensis SBZ3-12 and the whole genome sequenced strains of the same genus. The analysis of its metabolic pathway showed that there was a complete TCA cycle pathway, which could guarantee the production of malic acid. The comparative analysis of metabolic pathways revealed that the TCA cycle pathways of other strains of Dyella were incomplete. The gene encoding catechol-type iron carrier receptor may be involved in the transport of mixed iron carrier. Based on the CsrA (Carbon storage regulator) analysis of D.jiangningensi.sSBZ3-12 and other species in ExPASy ProtParam Server,Pole Bioinformatique Lyonnais Network Protein sequence analysis and SWISS-MODEL online databases, it was found that the primary structure of CsrA was not significantly different, but the tertiary structure of CsrA was obviously different. It may perform specific functions in different strains and lay a foundation for elucidating the molecular biological mechanism of the weathering minerals of this strain. Identification of a mineral weathering bacterium A31 as a new species of the genus Sinomonas by multiphasic taxonomy, named Sinomonas susongensis sp.nov.
【学位授予单位】：南京农业大学
【学位级别】：硕士
【学位授予年份】：2015
【分类号】：P512.1;Q93

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