Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School QMC, Derby Road, Nottingham NG7 2UH, UK.
BMC Genomics. 2012 Nov 27;13:670. doi: 10.1186/1471-2164-13-670.
Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.
To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.
The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.
进化使蛭弧菌捕食性细菌能够入侵其他细菌，消化并复制，从而将其密封在内部，防止与周围环境中的生物共享营养物质。蛭弧菌以前被描述为“专性捕食者”，因为只有通过突变，通常在基因 bd0108 中，约有 1/1x10(7)的捕食性实验室株的蛭弧菌才会转变为不依赖猎物的生长。之前对 B. bacteriovorus 株 HD100 的基因组分析表明，通过裂解酶对猎物 DNA 的捕食性消耗使蛭弧菌比其他细菌更不可能通过横向基因转移（LGT）获得 DNA。然而，Doolittle 和 Pan 小组通过计算机预测，古老的和最近的侧向基因转移都进入了 B. bacteriovorus HD100 基因组。
为了验证这些预测，我们通过用大肠杆菌猎物细胞进行富集培养，从台伯河分离出一种捕食性细菌——这是 LGT 的一个很好的潜在来源，因为它富含多种细菌和有机污染物。该分离株被鉴定为 B. bacteriovorus，并命名为菌株 Tiberius。不同寻常的是，这种台伯河菌株同时表现出对有机营养物质的不依赖猎物的生长和对活猎物的捕食性生长。尽管有不依赖猎物的生长，但 bd0108 的同源物没有典型的不依赖猎物型突变。这种双重生长模式可能反映了河流的高碳含量，并使 B. bacteriovorus Tiberius 与存在的其他细菌有了更长时间的非捕食接触。尽管 HD100 和 Tiberius 基因组具有不同的培养历史（陆地/新鲜分离的水生），但它们的基因内容非常相似；但基因内容的差异表明存在基因组流动和 LGT。基因内容比较支持之前发表的关于 HD100 菌株中 LGT 的计算机预测，大量保守的基因预测具有古老的 LGT 起源，但很少保守预测为最近获得的富含 AT 的基因。
B. bacteriovorus Tiberius 菌株的自然生态位和双重捕食性以及不依赖猎物的生长，使其与其他海洋和淡水细菌有广泛的非捕食性接触，这些细菌的基因组中存在 LGT。因此，尽管它们拥有大量的 DNA 裂解酶；但在自然生态位中，蛭弧菌并不总是捕食者，它们的基因组通过从其他细菌中获取完整的基因而形成。
