与底物生物降解相关的新鞘属细菌在湖泊等环境中普遍存在,土壤,海,木材和沉积物。为了更好地了解与它们的广泛分布和代谢多功能性相关的特征,我们报告了夜蛾的全基因组序列。THN1,一种先前由Jiang等人分离的微囊藻毒素降解菌株。(2011)来自太湖蓝藻水样,中国。我们对Novosphingobiumsp。进行了基因组比较分析。从GenBank下载的THN1与21种其他降解的Novosphingobium菌株。使用16SrRNA基因构建系统发育树,核心基因,蛋白质编码序列,和整个基因组的平均核苷酸同一性。直系同源蛋白质分析表明,22个基因组包含674个核心基因,每个菌株都包含高比例的分布基因,这些基因由菌株的子集共享。对其基因组可塑性的检查发现,大量的插入序列元件和基因组岛分布在染色体和质粒上。我们还比较了Novosphingoum蛋白编码基因的预测功能谱。柔性基因和所有蛋白质编码基因产生相同的热图簇。COG注释用于生成与降解的化合物相关的树状图。此外,从KEGG途径预测的代谢谱表明,大多数基因参与中心碳代谢,氮,磷酸盐,硫酸盐代谢,能量代谢和细胞迁移率(62.5%以上)位于染色体上。然而,许多参与降解途径的基因(21-50%)位于质粒上。在22个新鞘氨脂菌株中,芳烃降解单加氧酶和双加氧酶的丰度和分布各不相同。微囊藻毒素降解mlr基因簇的比较分析为该簇的水平获得提供了证据。Novosphingoumsp.THN1基因组序列包含对微囊藻毒素降解至关重要的所有功能基因,并且mlr基因簇与从蓝藻繁殖水中分离的其他微囊藻毒素降解属的序列具有高度的序列相似性(≥85%)。我们的结果表明,新鞘氨醇物种具有较高的基因组和功能可塑性,根据环境变化重新排列它们的基因组,并通过它们所接触的底物来塑造它们的代谢谱,更好地适应他们的环境。
Bacteria in genus Novosphingobium associated with biodegradation of substrates are prevalent in environments such as lakes, soil, sea, wood and sediments. To better understand the characteristics linked to their wide distribution and metabolic versatility, we report the whole genome sequence of Novosphingobium sp. THN1, a microcystin-degrading strain previously isolated by Jiang et al. (2011) from cyanobacteria-blooming water samples from Lake Taihu,
China. We performed a genomic comparison analysis of Novosphingobium sp. THN1 with 21 other degradative Novosphingobium strains downloaded from GenBank. Phylogenetic trees were constructed using 16S rRNA genes, core genes, protein-coding sequences, and average nucleotide identity of whole genomes. Orthologous protein analysis showed that the 22 genomes contained 674 core genes and each strain contained a high proportion of distributed genes that are shared by a subset of strains. Inspection of their genomic plasticity revealed a high number of insertion sequence elements and genomic islands that were distributed on both chromosomes and plasmids. We also compared the predicted functional profiles of the Novosphingobium protein-coding genes. The flexible genes and all protein-coding genes produced the same heatmap clusters. The COG annotations were used to generate a dendrogram correlated with the compounds degraded. Furthermore, the metabolic profiles predicted from KEGG pathways showed that the majority of genes involved in central carbon metabolism, nitrogen, phosphate, sulfate metabolism, energy metabolism and cell mobility (above 62.5%) are located on chromosomes. Whereas, a great many of genes involved in degradation pathways (21-50%) are located on plasmids. The abundance and distribution of aromatics-degradative mono- and dioxygenases varied among 22 Novosphingoibum strains. Comparative analysis of the microcystin-degrading mlr gene cluster provided evidence for horizontal acquisition of this cluster. The Novosphingobium sp. THN1 genome sequence contained all the functional genes crucial for microcystin degradation and the mlr gene cluster shared high sequence similarity (≥85%) with the sequences of other microcystin-degrading genera isolated from cyanobacteria-blooming water. Our results indicate that Novosphingobium species have high genomic and functional plasticity, rearranging their genomes according to environment variations and shaping their metabolic profiles by the substrates they are exposed to, to better adapt to their environments.