基于16S rRNA和RubisCO基因对嗜酸硫杆菌的系统发育及多样性

Phylogenetic and diversity analysis of Acidithiobacillus spp. based on 16S rRNA and RubisCO genes homologues

摘要:

[目的] 明确不同地理来源的Acidithiobacillus spp.种群是否表现出显著的地域性和异域物种形成;为了解微生物谱系地理、多样性维持机制和微生物分子地理学提供基础数据。[方法] 采用16S rRNA基因、核酮糖-1,5-二磷酸羧化酶/加氧酶(RubisCO)功能基因序列同源性分析构建相应的系统发育树,分析Acidithiobacillus spp.种群的遗传多样性。[结果] 从3个不同的地域分离到35株菌聚为5大类群,其中菌株YNTR4-15可能是铁氧化细菌(Leptspirillum ferrooxidans),菌株HBDY3-3被鉴定为另一铁氧化细菌(Leptospirillum ferrodiazotrophum);有4株可能是Acidithiobacillus ferrivorans;6株是Acidithiobacillus ferridurans,其余菌株均被鉴定为Acidithiobacilus ferrooxidan。对26株代表性菌株的RubisCO I型cbbL基因和II型cbbM基因的分析,发现19株菌具有双拷贝cbbL基因,分别为cbbL1和cbbL2基因;7株菌只检测到了cbbL1。cbbL1和cbbL2基因都有3个序列型;而cbbM基因是单拷贝。RubisCO基因的密码子偏爱性不强。[结论] 分离自3个地域的菌株16S rRNA/RubisCO基因存在序列差异,Acidithiobacillus spp.种群存在显著的遗传多样性。嗜酸硫杆菌分离菌株基于16S rRNA基因的系统发育树和RubisCO基因的发育树不一致。

Abstract:

[Objective] The purpose of the study was to reveal geographic region-related Acidithiobacillus spp. distribution and allopatric speciation. Phylogenetic and diversity analysis was done to expand our knowledge on microbial phylogeography, diversity-maintaining mechanisms and molecular biogeography. [Methods] We amplified 16S rRNA gene and RubisCO genes to construct corresponding phylogenetic trees based on the sequence homology and analyzed genetic diversity of Acidithiobacillus spp.. [Results] Thirty-five strains were isolated from three different regions in China (Yunnan, Hubei, Xinjiang). The whole isolates were classified into five groups. Four strains were identified as A. ferrivorans, six as A. ferridurans, YNTR4-15 Leptspirillum ferrooxidans and HBDY3-31 as Leptospirillum ferrodiazotrophum. The remaining strains were identified as A. ferrooxidans. Analysis of cbbL and cbbM genes sequences of representative 26 strains indicated that cbbL gene of 19 were two copies (cbbL1 and cbbL2) and 7 possessed only cbbL1. cbbM gene was single copy. In nucleotide-based trees, cbbL1 gene sequences of strains were separated into three sequence types, and the cbbL2 was similar to cbbL1 with three types. Codon bias of RubisCO genes was not obvious in Acidithiobacillus spp.. [Conclusion] Strains isolated from three different regions in China indicated a great genetic diversity in Acidithiobacillus spp. and their 16S rRNA/RubisCO genes sequence was of significant difference. Phylogenetic tree based on 16S rRNA genes and RubisCO genes was different in Acidithiobacillus spp..